Editor's note: CNN's Kaj Larsen served as an active duty member of the U.S. Navy SEALs for five years and was trained in combat diving. For more on this story and others, check out "CNN Presents," Saturday night at 8 p.m. ET/PT.

San Diego (CNN) -- In a little-known part of the counter-terrorism world, one of the most effective detection systems is a 600-pound animal that works for about 20 pounds of fish a day.

Since the 1960s, the United States and a handful of other countries have trained dolphins and sea lions to detect sea mines and swimmers, and to recover inert torpedoes and testing objects used in Naval exercises.

Program officials estimate that the sea lions in the Marine Mammal Program have recovered millions of dollars of U.S. Naval torpedoes and instrumentation dropped on the sea floor.

The U.S. Navy kept its Marine Mammal Program a secret until the 1990s, and this spring CNN became one of only a handful of media outlets to see firsthand how the program works.

Watch Kaj take part in U.S. Navy marine mammal exercise

The program trains about 75 Pacific bottlenose dolphins, with natural biosonar that tracks better than any manmade device; and 35 California sea lions, with supurb underwater eyesight.

Not only do these trained marine mammals track and retrieve millions of dollars in U.S. military equipment, they are also helping to save lives.

The Navy won't disclose whether the dolphins and sea lions have effectively intercepted terrorists attempting to do harm to any U.S. facilities.

Either way, "it serves as a deterrent effect," says Christian Harris, operations supervisor for the program.

When animals protect

The mammals can be deployed via C-130 cargo aircraft to perform their missions anywhere in the world within 72 hours. They have been used in exercises from Alaska to Hawaii, operating in great temperature and environmental ranges. They also have the capability to operate off vessels.

Dolphins most recently were deployed in the Iraq war, performing mine detection and clearance operations in the Persian Gulf to ensure safe passage for humanitarian ships delivering aid. Some of these Iraq war "veterans" are now back home, tasked with a new mission: guarding nuclear submarines in their homeports of Bremerton, Washington, and Groton, Connecticut.

A key part of the training program is teaching these mammals how to intercept potentially hostile swimmers.

There is an entire domain of port and harbor security devoted to anti-combat swimmer or swimmer defense. Combat diving or swimming is practiced by a small contingent of special operations forces around the world.

Using an underwater breathing apparatus, at night, is a very stealthy way to come upon a target unannounced and inflict violence of action with the element of surprise. The German Kampfschwimmers, Israel's Shayatet 13, and the U.S. Navy SEALs are generally considered the premier units that train and conduct combat swimmer operations around the world.

The Marine Mammal Program was conceived to defend against these kinds of attacks from hostile nations.

The program is also positioned to defend against lone swimmer terrorist attacks as well.

In 2002, classified reports from the intelligence community, gleaned from interrogations of suspects in Afghanistan, warned that al Qaeda was planning on using scuba divers to attack U.S. Navy vessels in port or at anchor.

And just this week a picture emerged on the Facebook page of Oslo terror suspect Anders Behring Breivik, holding a modified assault rifle in what appears to be a combat diving set-up.

How the program started

In the 1960s, the U.S. Navy began studying the hydrodynamics of a Pacific white-sided dolphin in an effort to improve torpedo performance. The Navy quickly realized that the incredibly efficient biosonar of the dolphin was excellent for detecting hard-to-find objects -- and people -- underwater.

For the next quarter-century, the U.S. Navy secretly honed the technique of using mammals to find both underwater objects, detect mines and combat swimmers. The Navy deployed dolphins to Vietnam and the Persian Gulf to perform the swimmer interdiction mission.

In the 1990s, the U.S. military declassified the Marine Mammal Program and since then, it has been headquartered at the Point Loma Naval Base in San Diego.

The program is managed jointly by the Naval Warfare Systems Center Pacific and military explosive experts, who are the backbone of the program.

In addition, civilian marine biologists, veterinarians, scientists and handlers are involved in the program. Researchers from institutions like Sea World to UC San Diego regularly collaborate with them for research purposes.

The program has an annual operating budget of $20 million, according to Marine Mammal Program director Mike Rothe who expressed confidence that the program's future funding is not at risk.

"We don't anticipate any impacts to our budget based on current issues in D.C.," Rothe said.

Dogged by accusations of animal mistreatment and conspiracy theories that the animals are used for offensive operations like mine placement and swimmer attack, the U.S. Navy has been slowly allowing access to the program.

In April, CNN got a rare opportunity to witness firsthand how accurate these animals are at detecting possible threats.

Trying to outsmart a dolphin

Armed with an inert limpet mine, I dove into the chilly waters of San Diego bay to perform five mock attacks on an experimental Navy ship docked to a pier to see how well these dolphins can find potential attackers in the water.

Both as a surface swimmer and using scuba gear, my experience was identical. I'd progress toward the ship and out of the murky waters of the bay I would feel an aggressive bump -- sort of like getting hit by a battering ram -- indicating the dolphin had marked me and that security forces were on their way to my location.

Despite all my efforts at concealment, I was an easy target for the dolphin in its natural environment.

Later, I was intercepted by a sea lion who attached a clamplike device to my leg -- allowing the security boat to reel me in.

The final score of my day of training in the bay: mammals 5, combat swimmer 0.

While it seems strange that in this digital era, there's such a seemingly lo-fi approach to guard the Navy's most sophisticated and expensive assets. But according to Rothe, nothing in today's hi-tech world can compete with these mammals' biosonar abilities.

"I hope that one day there is a robot or a UUV [unmanned underwater vehicle] that makes the mammal program obsolete," he said. "But right now this is the best thing out there."