Historians and architects from the Naval History and Heritage Command in the District had joined forces with Allen last year to revisit the tragedy.
The ship sank in 15 minutes on July 30, 1945, in the war's final days. It took the Navy four days to realize that the vessel was missing.
About 800 of the crew's 1,200 sailors and Marines made it off the cruiser before it sank. But almost 600 of them died over the next four to five days from exposure, dehydration, drowning and shark attacks. Nineteen crew members are alive today, the Navy command said in a news release.
The Indianapolis had just completed a top-secret mission to deliver components of the atomic bomb "Little Boy" to the island of Tinian. The bomb was later dropped on the Japanese city of Hiroshima.
In a statement on its website, the command called the shipwreck a "significant discovery," considering the depth of the water.
"While our search for the rest of the wreckage will continue, I hope everyone connected to this historic ship will feel some measure of closure at this discovery so long in coming," Allen said in a statement. His research vessel, Petrel, has state-of-the-art subsea equipment that can descend to depths like those at which the ship was found.
The cruiser's captain, Charles Butler McVay III, was among those who survived, but he was eventually court-martialed and convicted of losing control of the vessel. About 350 Navy ships were lost in combat during the war, but he was the only captain to be court-martialed. Years later, under pressure from survivors to clear his name, McVay was posthumously exonerated by Congress and President Bill Clinton.
The shipwreck's location had eluded researchers for decades.
The coordinates keyed out in an S.O.S. signal were forgotten by surviving radio operators and were not received by Navy ships or shore stations, the Navy command said. The ship's mission records and logs were lost in the wreck.
Researchers got a break last year, however, when Richard Hulver, a historian with the Naval History and Heritage Command, identified a naval landing craft that had recorded a sighting of the Indianapolis hours before it was sunk. The position was west of where it was presumed to be lying. The team was able to develop a new estimated position, although it still covered 600 square miles of open ocean.
The ship is an official war grave, which means it is protected by law from disturbances. Naval archaeologists will prepare to tour the site and see what data they can retrieve. No recovery efforts are planned.
Hulver and Robert Neyland, the command's underwater archaeology branch head, wrote on the website that "there remains a lot we can learn."
"From the sinking to the battle damage and site formation processes, we hope to gain a better understanding about the wreck site and how we can better protect USS Indianapolis to honor the service of the ship and crew."