By Mark Potter, Correspondent, NBC News

TUCSON, ARIZ. – On a helicopter inspection tour above the rugged mountains and vast desert in southern Arizona, Commander Jeffrey Self of U.S. Customs and Border Protection reflected on how much security has improved along the U.S.-Mexican border during his long career.

"After the vehicle barriers were built, and with the checkpoints going up, we're experiencing zero [undocumented immigrant] drive-throughs in an area where we were having 30, 40, 50 in a 24-hour period," he said, pointing to miles of vehicle barriers placed in the desert along the frontier.

U.S. Border Patrol has greatly reduced the number of cars and trucks loaded with people and drugs driving across the desert from Mexico into the United States. That, Self explained, has freed agents to focus their attention on immigrant and drug smugglers who walk across the border.  In the meantime, he added, authorities have also greatly reduced the number of hiking trails used by smugglers.

"In Arizona we have been very successful in increasing border security," Self said. "Over the course of many years now we've been resourced with tactical infrastructure, technology and personnel and they've been employed in a fashion that's gotten us greater results."

While conceding there are still many areas where drug and immigrant smugglers cross illegally into the U.S. -- often on private ranch land -- Self argued the threat has decreased dramatically and will continue to do so.

Mark Potter/NBC News

The U.S. border vehicle barrier used by authorities to stop trucks and cars from crossing the Mexican border in southern Arizona.

As the national debate over comprehensive immigration reform plays out, the question looms: just how secure is the U.S. border with Mexico? The answer appears to be mixed, with definite improvements nationwide and a downward trend in illegal immigration in most places – especially in the cities. But there are some areas, in rural Arizona and Texas, where residents insist the border is neither secure nor safe.

Gary Thrasher, a veterinarian and rancher in southern Arizona near Bisbee, says the rural border area where he works is actually less safe now than it was years ago, because of an increase in the number of armed drug and immigrant smugglers.

When the federal government increased security in the border cities, he said, it had the negative effect of forcing the smugglers to move to the large rural areas.

"The border statistically is securer than ever.  That means nothing,” he said.  “That's like saying we fixed this whole bucket, except for this hole down here.  You know it's still not going to hold water."

U.S. officials: look to the numbers 

Homeland Security Secretary Janet Napolitano frequently travels to the Southwest border and has made appearances before Congress where she has touted the recent improvements in border security and argued for passage of a comprehensive immigration bill.

"Fewer people are trying to emigrate illegally into this country than in four decades,” she testified before a U.S. Senate committee earlier this year. “What I know is that apprehensions are low, because attempts are low. Drug seizures, contraband seizures, all the numbers that need to be up are up."

In the year 2000, agents along the length of the Southwest border reported detaining 1,643,679 immigrants for allegedly entering the country without proper documentation.  Twelve years later, in 2012, that number had plummeted to 356,873, a decrease of 78 percent.

"San Diego and the Mexican border used to be the most lawless, violent places across the face of the earth with thousands of cross-border migrants on a given day,” said retired Gen. Barry McCaffrey, the former head of the Office of National Drug Control Policy. “We put in triple fencing and adequate Border Patrol and Coast Guard and it stopped."

Ranchers: rural border areas not secure

Critics of the administration's position on border security, however, say that while the overall apprehension numbers are down, they don't fully reflect the reality in areas where smugglers and immigrants still routinely make the illegal crossing into the United States from Mexico.

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An NBC hidden camera captures footage of border-crossers hiking across private U.S. ranch land in southern Arizona during late March.

On a small ranch near the border in southwestern Arizona, a mother of several children spoke under the condition of anonymity.  She fears what she described as an increase in drug and immigrant smugglers crossing her land by day and night.

"You're still having to pack a gun everywhere with you and make sure your kids can't go outside to play unless you are watching them." she said.  "The border is not secure. The Border Patrol doesn't have a very strong presence out here."

Texas police: a rise in immigrant smuggling

In the small town of San Juan, Texas, a few miles north of the Mexican border, Police Chief Juan Gonzalez toured some of the human stash houses his officers recently uncovered. They had been used to hide immigrants from all over the world who were smuggled across the border into the United States.

Gonzalez says his department has never dealt with as many undocumented immigrants as it encounters now. 

"In the past three years we've seen an increase.  And it's not a steady increase, it's a massive increase," he said.  "Too many people are getting through.  We've got too many holes in the border and we don't have enough manpower to make sure we secure the border."

About 75 miles north of the border, in Falfurrias, Texas, Benny Martinez, the chief deputy of the Brooks County Sheriff's Office, says his area is also deeply affected by a recent rise in illegal immigration. 

“The trending is going up,” he said.  “It hasn’t gone down at all, not here.”

Last year, officials and ranchers there found the bodies of 129 immigrants who died in the harsh terrain, presumably after crossing the border illegally.  Dozens are still unidentified and are buried in a local cemetery.  Some of the metal markers on the graves read, "Unknown Female" and "Unknown Remains."  One says, simply, "Bones."

Martinez does not believe the U.S.-Mexican border is at all secure in South Texas, given the rise in illegal immigration in Brooks County. 

"It's steady and I don't think it's going to go down, it's not going to happen anytime soon," he said.

PHOTOS: Border patrol faces surge in rural Texas border crossings

Ranchers like Linda Vickers, who lives just north of a Border Patrol highway checkpoint near Falfurrias, said she regularly sees, and often photographs, illegal immigrants cutting across her land as they try to evade the agents. 

“I’m seeing groups of 10, groups of 20 and I’m seeing them more often,” she said.

When asked about Obama administration claims that the border is more secure now, Vickers said that while it appears to be true elsewhere in the country, it’s not the case where she lives. 

“In the state of Texas, in the Rio Grande Valley, the border is not secure and I don’t think you’ll find a person, a real person, to say it’s secure,” she said.

Border patrol: South Texas a problem area

In South Texas, in the Rio Grande Valley sector, immigrant apprehensions rose 65 percent from the years 2011 to 2012 -- from 59,243 to 97,762, according to U.S. Border Patrol -- bucking the national trend of falling immigration numbers. 

This year, statistics reveal the Rio Grande Valley apprehension numbers have climbed even further, rising 55 percent compared to this time in 2012. 

Federal agents believe it reflects a recent increase in people fleeing the poverty, drug gangs and violence in Central America.

Privately, some agents say that, despite their great success in making more apprehensions, thousands of immigrants crossing the border illegally in South Texas still slip past them.

A majority of people involved in the security debate agree that most of the U.S. cities along the border are now much safer than they used to be and have much lower crime rates, thanks to high fences, increased monitoring technology and thousands of Border Patrol and other federal agents deployed there.  

But McCaffrey says U.S. officials need to do more for the rural areas.

“You have to give the Border Patrol and Customs and Border Protection the dollars and the technology to protect the American frontier,” he said.  “We’ve got to do it.  We owe it to the American people.”

This story was originally published on Thu May 2, 2013 11:29 AM EDT

MALIBU, CALIF. -- On a starry night in the hills overlooking the Pacific Ocean north of Los Angeles, a two-man California National Guard special forces surveillance team sets up a sophisticated night scope. Their mission is to search the horizon and the waters below for an increasing number of Mexican drug traffickers offloading multi-ton loads of marijuana--and sometimes illegal immigrants--on remote U.S. beaches.

"These service members are the eyes and ears of federal law enforcement here," said Lt. Kara Siepmann, of the Guard's National Drug program. When asked about what specifically they are looking for, one of the surveillance team members said, "We're looking for blacked out vessels and any suspicious activity we can find, any unusual boats coming through the area." 

Used to smuggle drugs from Mexico, this panga boat was captured near Huntington Beach, Calif., in August 2011. The faces of the three men being arrested have been obscured at the request of the HSI.

The soldiers work quietly and in the dark, aware that the Mexican traffickers have their own spotters here watching out for U.S. law enforcement personnel. "They don't want to land where the National Guard or the Border Patrol are looking for them," said Siepmann.

Turning fishing boats into drug boats
In the last few years, law enforcement officials said they have seen a considerable spike in smugglers loading drugs or immigrants onto boats in Mexico's northern Baja Peninsula, then motoring north to offload their illegal cargo along a 300-mile-long stretch of California beaches, sometimes within sight of the many luxury homes on the coastline. 

Courtesy of HSI/ICE

Used to smuggle drugs from Mexico, this panga boat was found in California's Ventura County in January 2012.

Related: Debate rages over Mexico 'spillover violence' in U.S.

Federal agents said this is the latest smuggling technique employed by Mexico's notorious Sinaloa drug cartel, headed by that country's most-wanted criminal, Joaquin "El Chapo" Guzman. The boats are small, open-hulled commercial fishing boats called pangas, which are commonly found in the inshore waters of Mexico and Central America. 

With their low profiles, the pangas are hard to spot in open water, but they can carry a large payload. Sometimes these 30- to 40-foot boats will have as many as four outboard engines, allowing them to outrun most vessels used by the authorities.

"The trend is pretty much going straight up," said Lt. Stewart Sibert, the captain of the US Coast Guard Cutter Halibut, which patrols in search of Mexican smugglers near the California coast. 

"The past few months have been very busy for us," he said. "We caught more drugs in these past two months than in the past two years."

According to arrest statistics reported by U.S. Immigration and Customs Enforcement, or ICE, there were 183 known "events" in fiscal year 2011 along the California coast involving the maritime smuggling of drugs or immigrants, up considerably from the previous three years. During the first seven months of this fiscal year, there have already been 113 such events as the numbers climb even faster than last year.

"We're seeing four and five tons of drugs come in per run and we're seeing dozens of runs. It's almost one or two per week at this point," said Sibert.

A dangerous trade heading north
Law enforcement officials have argued the rise in maritime smuggling is a direct result of their crackdown on smuggling operations along the U.S. land border with Mexico. As they first interdicted smuggling boats headed for beaches in southernmost California, near San Diego, they began to see the traffickers moving farther north to drop off their loads, which are then distributed across the country.

Related: Patrolling 'smugglers' alley' by air along the Rio Grande

"As we stop them in one area, they’re trying to go around us. We're sort of leapfrogging up the coastline," said Sibert. Recently, an abandoned panga and a hidden marijuana stash were found near San Simeon, Calif., more than 300 miles from the Mexican border.

"They go far out to sea to try to evade interdiction efforts along the border," said Claude Arnold, the special agent in charge for ICE Homeland Security Investigations. "They typically go 100 miles out or farther due west, and then they come north," to reach the U.S. coastline.

While the panga boats are considered relatively stable when used for fishing in calm inshore waters, officials said, they can be quite dangerous in rougher waters offshore, especially if they are overloaded with drugs or illegal immigrants. The boats rarely have adequate safety equipment and authorities speculate that many may have been lost at sea, along with their passengers.

Courtesy of HSI/ICE

Used to smuggle drugs from Mexico, this panga boat was found on California's Leo Carrillo Beach in August 2011.

"It's a direct indication of these criminal smuggling organizations' complete disregard for human life. They are driven by profit and nothing else," said Troy Matthews, of the U.S. Border Patrol in San Diego. "You'll have somebody driving the ship who is not necessarily highly-trained. You'll have poorly maintained vehicles that will break down and subsequently they are loitering out at sea for days."

A border security threat
As they find more boats on the beaches and make more arrests, U.S. authorities are learning more about how the smuggling operation work, and the degree to which they are coordinated with land-based trafficking operations.

"We've seen some pangas that run directly up onto the beach and upload their cargo," said Sibert. "And then we've seen some that will come in and transfer their load to recreational boats that look less suspicious and try to run them directly into the marinas and yacht clubs."

Many times the panga boat operators will land at night on remote beaches near roads or a highway where they met by other members of the smuggling group. "There's usually an offloading team that will have a rental boxcar, U-Haul, or something of that nature to take the payload and transport it to a stash house where an organization begins the distribution process," said Arnold. 

A particular concern voiced by many U.S. authorities is the potential national security threat these boats and smugglers represent.  "They're just as willing to smuggle perhaps a weapon of mass destruction as they are a load of narcotics," warned Arnold.  "And they're just as willing to smuggle a terrorist as people coming here to work."  

To coordinate their interdiction efforts, federal, state and local law enforcement officials have formed a coastal-area task force. "As they adapt, we will adapt, and they'll continually try to find new ways to get contraband and people into the country, and we're going to be right there nipping at their heels," said Arnold.

Authorities conceded, however, that so far they are seeing no let-up in the Mexican maritime smuggling trade, and, in fact, are actually seeing bigger drug loads on boats now than in recent years.

"It's a huge challenge," said Matthews, from the U.S. Border Patrol. "It's an immense geographical area that we have to cover. There is not only single agency that can cover it by itself."

Pope Benedict XVI is on a state visit to Cuba this week hoping to highlight the role of the Roman Catholic Church on the Communist island, as well as making subtle push for change.

Benedict called for "renewal and hope, for the greater good of all Cubans," during a speech on Tuesday. "I have also prayed to the Virgin for the needs of those who suffer, of those who are deprived of freedom, those who are separated from their loved ones or who are undergoing times of difficulty."

But the Cuban government was quick to say that there "will not be political reform" in the country as a result of the pope's visit.

NBC News' Mark Potter is in Havana. He answered interesting reader questions about Benedict's visit earlier today.

Click below to replay the chat.

HAVANA, Cuba – At the historic San Francisco de Paula church, in a working-class neighborhood of Havana, Auxiliary Bishop Alfredo Petit recently walked the long hallways where priests, nuns and lay workers were busy caring for some of Cuba's elderly and infirm and also operating an orphanage. Outside the church is a sign welcoming the pope: "Bienvenido a Cuba Benedicto XVI."

Petit hopes during the pontiff's three-day visit to the island his messages will provide an important boost for the Cuban Catholic Church and perhaps even inspire some gradual changes in Cuban society.  "I don't know what the words will be, but I think they will suggest more respect for human dignity,” he said.

Since the Cuban revolution in 1959, the Catholic Church has struggled to raise its public profile here. For decades, under the Marxist government of Fidel Castro, the church was ostracized and believers were punished. The country was officially declared atheist until the government loosened that description in the 1990's.

But, with Fidel Castro out of power now and his younger brother, Raul, in charge, the church has become much more accepted by the government. Recently, Cuban Cardinal Jamie Ortega negotiated the release of more than 100 political prisoners, although he was criticized by human rights activists after most of the prisoners were sent into exile.

"The church has now been accepted as a legitimate and important interlocutor of the government on sensitive topics like freeing political prisoners, the conditions of those in prison, the treatment of dissidents," said Jorge Dominguez, a professor at Harvard University's Kennedy School of Government.  "This is a wholly unprecedented role for the Roman Catholic in Cuba for the past half century."

With funds and supplies donated from overseas, the church also provides much-needed social services now as the government struggles to reshape Cuba's troubled economy. Church-run food banks and retirement homes along with medicine distribution centers have become lifelines many of Cuba's extremely poor.

"It is very convenient for the government that the church will engage in activities providing for people in need," said Juan Clark, a Miami Dade College professor emeritus and an expert on the Cuban Church.

Still, tensions remain over the issues of religious and personal freedoms.

Last year, the church convinced state security to stop harassing the "Ladies in White," a church-based dissident group. However, two weekends ago, three-dozen members of the group were detained during a protest march in Havana. Ironically, 13 other dissidents who recently sought sanctuary in a Havana basilica were turned over by church officials to police, sparking accusations the church may have actually grown too close to Cuban leaders.

Pope Benedict is now urging Cuba to find new alternatives to Marxism – patiently and peacefully – as the Catholic Church maintains a delicate relationship with the Communist government here. 

The pope’s first stop on Monday will be Santiago de Cuba, the island's second city where he will celebrate a large open-air mass. On Tuesday, he visits the town of El Cobre, home to a tiny wooden statue of Our Lady of Charity, a symbol revered by all Cubans – Catholic and non-Catholic alike.

Later that day he flies to Havana for what is expected to be a meeting with both Raul and Fidel Castro. On Wednesday morning he will celebrate another mass in Havana before departing the country.