SAN FRANCISCO >> In 2005, the USS America aircraft carrier was towed out to sea on her final voyage. Hundreds of miles off the Atlantic coast, U.S. Navy personnel then blasted the 40-year-old warship with missiles and bombs until it sank.

The massive Kitty-Hawk class carrier — more than three football fields long — came to rest in the briny depths about 300 nautical miles southeast of Norfolk, Va.

Target practice is now how the Navy gets rid of most of its old ships, an Associated Press review of Navy records for the past dozen years has found. And they wind up at the bottom of the ocean, bringing with them amounts of toxic waste that are only estimated.

Navy documents state that among the toxic substances left onboard the America were more than 500 pounds of PCBs or polychlorinated biphenyls, a chemical banned by the U.S. in 1979, in part because it is long-lasting and accumulates throughout the food chain. Disposing of the carrier that served in the Vietnam War, Desert Storm and Desert Shield cost more than $22 million.

In the past 12 years, records show the Navy has used missiles, torpedoes and large guns to sink 109 old, peeling and rusty U.S warships off the coasts of California, Hawaii, Florida and other states. During the same period, 64 ships were recycled at one of six approved domestic ship-breaking facilities.

The Navy says target practice on actual military ships serves an important national security function, allowing for live-fire exercises and study of “weapons lethality.” But since the program’s inception, the AP found that the Navy has struggled to balance its military training needs with an environmentally sound way to send ships to the grave.

The program — called “Sinkex” for sinking exercise— has come under fire from environmentalists for the pollutants it introduces to the sea. The ship recycling industry complains about the jobs and revenues it takes away.

The Navy has performed these operations for decades, disposing of decommissioned ships with little public record of the toxins left onboard. Then in 1999, the Environmental Protection Agency ordered the Navy to better document toxic waste on the doomed ships, and in return the EPA exempted the military from federal pollution laws that prohibited such dumping in the ocean.

Now, new evidence from a Florida ship sinking site suggests these old warships can cause spikes in PCB levels in nearby fish. It spurred Florida officials to bar further dumping along their coast. And it has evoked a federal lawsuit alleging the EPA has failed to properly safeguard federal waters.

Along with the memories of sailors who once lived on these ghost ships, the massive boats each can contain thousands of pounds of PCBs, asbestos, lead, mercury and other harmful substances in keels, insulation materials, wiring and felt gaskets.

The EPA and federal Centers for Disease Control and Prevention say PCBs endure for years.

In humans, high levels are believed to increase the risk of certain cancers and, in pregnant or breast-feeding women, harm the developing brains of fetuses and infants. PCBs were once widely used in transformers and electrical equipment and they’ve turned up in fresh water fish and other foods as well.

Under its agreement with the EPA, the Navy must document how much toxic material is removed and how much is sent into the sea. But the AP review of the Navy’s year-end reports since 2000 found incomplete and inconsistent estimates of PCBs and other toxics.

For example, from 2000 to 2004, the Navy only reported the estimated weight of a certain type of felt gasket that contains PCBs, rather than all materials containing PCBs.

Throughout the records, ships of similar size and make showed different estimates of PCBs left onboard. In 2008, the Navy estimated that no PCBs remained on the nearly 7,000-ton USS David R. Ray, a destroyer that once operated in the Persian Gulf. But the previous year, a similar-sized vessel, the guided missile cruiser USS Jouett, was reported to contain more than 100-pounds of materials containing PCBs. The Navy did not comment on these apparent discrepancies.

“The Navy’s PCB volume estimates and self-reporting methods are questionable,” said Colby Self of the environmental group Basel Action Network, which along with the Sierra Club sued the EPA. “Yet the EPA continues to disregard the Navy’s self-reporting shortfalls and defend legal exemptions that allow the Navy to dump toxic waste ships at sea.”

The Navy says it costs $500,000 to $600,000 to remove toxics from ships before the target practice, although the total cost of the disposal exercises is much higher. Ship breaking companies say their price for recycling a large Navy vessel is typically tens of millions of dollars.

The Navy defended its cleaning and inventory process, saying it removes all liquid PCBs, thousands of gallons of fuel, mercury from instruments and other pollutants.

“The Sinkex program provides numerous benefits to the Navy by making target vessels available for at-sea live-fire exercises,” Navy spokesman Christopher Johnson said in an e-mail. “It provides opportunities for air, surface and subsurface forces to conduct weapons effect testing on actual combat ships.”

“Each vessel is put through a rigorous cleaning process that includes the removal, to the maximum extent practicable, of all materials which may degrade the marine environment,” he said.

In the 1990s, the Navy was forced to stop Sinkex for two years because of concern that the program ran afoul of the federal Toxic Substances Control Act’s prohibition of PCB releases.

At the time, many old Navy vessels were sent to ship-breaking facilities in Bangladesh and southeast Asia, where they were scrapped at a much cheaper price than U.S. yards. But, after an investigation by the Baltimore Sun uncovered environmental and workplace issues at those facilities, the U.S. government in 1998 banned overseas recycling.

The next year, EPA exempted Sinkex from federal toxic pollution laws, and the Navy resumed sinking old ships — at least 50 nautical miles from shore and at least 6,000 feet deep.

The agency’s chief at the time, Carol Browner, wrote in a Sept. 7, 1999 letter that failure to grant an exemption would “unnecessarily impede” the Sinkex program by opening the Navy up to environmental lawsuits. Browner said regulating Sinkex under the toxic control law would require too much of the agency’s resources.

An EPA spokeswoman declined to comment for this story, citing the ongoing litigation.

Sending PCBs and other chemicals to the ocean floor instead of recycling the ships runs counter to federal marine conservation efforts, said Peter deFur, a professor of environmental studies at Virginia Commonwealth University who sits on the Mid-Atlantic Fisheries Management Council, which oversees fisheries from New York to North Carolina.

“This excess in PCBs runs counter to all of our management objectives,” deFur said. “There’s the possible threat to public health from the PCBs that get into fish that people eat. And marine mammals are also at risk from elevated PCB levels in fish.”

PCB’s found in fish near an aircraft carrier sunk in 2006 as an artificial reef near Pensacola, Florida have raised concerns about the impacts, although the ship was located much closer to shore and in much shallower waters than Sinkex vessels.

Annual monitoring by the Florida Fish and Wildlife Conservation Commission of waters around the USS Oriskany concluded that fish around the carrier exceeded state and federal PCB standards in the first two years. Florida’s PCB limits are 50 parts per billion for safe human consumption— EPA standards are 20 ppb. Fish later collected saw a drop in those levels overall, but some still exceeded the EPA and Florida standards.

The PCB concentrations in fish have raised public health concerns that require more study to assess the long-term impacts, said Jon Dodrill, an environmental administrator with Florida’s commission. “Our agency has taken a stance that there will be no more large ships with regulated PCBs sunk in state or adjacent federal waters off of Florida,” Dodrill said.

Meantime, the nation’s ship breaking concerns have spoken out against Sinkex, saying it is costing the industry many millions of dollars and badly needed jobs.

Richard Jaross, co-owner of Esco Marine, Inc. in Brownsville, Tex., said his business would add jobs and revenue to the local economy if more Sinkex vessels were sent for recycling. He also believes the program is bad for the environment.

“The waters of the world aren’t dumping grounds for getting rid of old things. It’s totally irresponsible of our government to use them for target practice,” Jaross said.