More than 64 years after it was purposely sent to a watery grave, the sunken wreck of an “amazingly intact” World War II-era aircraft carrier was located by researchers in the waters off the Northern California coast, officials said Thursday.

The U.S.S. Independence operated in the Pacific in the early 1940s and was later used as a target ship in atomic bomb tests at Bikini Atoll in the Marshall Islands, where it sustained significant damage from shock waves, heat and radiation.

No longer functional as a warship, the Independence was moored at Hunters Point Shipyard, where the Navy used it to study decontamination processes, according to the National Oceanic and Atmospheric Administration.

By 1951, as the ship continued to age — and fears grew that it would sink — the Navy towed the Independence out to sea, where it was scuttled off the Farallon Islands. In the engine compartment, the Navy put 55-gallon drums of an unknown material, possibly radioactive waste, said James Delgado, the chief scientist on the Independence mission.

The ship has rested on the ocean floor ever since. Despite more than six decades in the unforgiving Pacific waters, the carrier looks little worse for wear, Delgado said.

“After 64 years on the seafloor, Independence sits on the bottom as if ready to launch its planes,” Delgado said. “This ship fought a long, hard war in the Pacific, and after the war, was subjected to two atomic blasts that ripped through the ship.”

Researchers discovered the wreck in March using an autonomous underwater vehicle — a drone — called the Echo Ranger, provided by Boeing. The expedition was part of a two-year archaeological mission to locate and study sunken ships in and around the Gulf of the Farallones National Marine Sanctuary, which encompasses nearly 3,300 square miles of ocean beyond the Golden Gate Bridge.

At a depth of roughly 2,600 feet, the Independence is thought to sit the deepest among an estimated 300 wrecks in the study area.

Using sonar, researchers zeroed in on the location of the Independence, and, once they found it, determined that the ship was largely whole, resting upright slightly on its starboard side, with holes in the flight deck. Through one of the holes, a shape that appears to be an aircraft is visible in the grainy sonar images captured by the unmanned sub.

“By using technology to create three-dimensional maps of the seafloor and wrecks like Independence, we can not only explore but share what we’ve learned with the public and other scientists,” said Frank Cantelas, an archaeologist with NOAA’s Office of Ocean Exploration.

Pictures of the ship from 1951 show the flight deck buckled from shock waves sustained in the atomic blasts. The condition of the wreck is a testament to the quality of shipbuilding in the mid-20th century, Delgado said.

“It is a reminder of the industrial might and skill of the 'greatest generation’ that sent not only this ship, but their loved ones to war,” he said. “This boat was built to take a pounding, and the fact that it’s still together is pretty remarkable.”

Delgado, who authored a report on the ships that were sunk as part of the tests at Bikini Atoll, said there were no plans to enter the Independence or to remove the 55-gallon drums. He said the Navy dumped drums of hazardous and radioactive waste in the sanctuary between 1946 and 1970.

The Gulf of the Farallones sanctuary and the surrounding waters are home to the largest breeding seabird rookery in the continental United States, numerous species of whales and great white sharks, among other sensitive species.

Kale Williams is a San Francisco Chronicle staff writer. E-mail: kwilliams@sfchronicle.com Twitter: @sfkale