Deep-sea explorers scouring the world’s oceans for sunken Second World War ships have uncovered the wreck of a Japanese aircraft carrier destroyed in the pivotal Battle of Midway.

Fought in June 1942, the clash saw US aircraft carriers ambush their Japanese foes and sink all four opposing Imperial Navy (IJN) flattops thanks partly to intelligence gained through intercepted communications.

The crew of the Petrel research vessel, in conjunction with the US Navy, revealed on Friday that it had found the Japanese carrier Kaga lying 5.4km beneath the waves. This week, the crew is sending robots into the abyss to investigate what may be another wreck site.

The expedition was started by the late Paul Allen, the billionaire co-founder of Microsoft, working with officials around the world to locate and document sunken ships, of which it has found 31 so far. It is illegal to otherwise disturb the underwater US military grave sites, and their precise coordinates are secret.

Eerie footage released by the Petrel team on Friday revealed the twisted wreck of the Kaga, which was finally tracked down after scans of some 500 nautical miles inside the Papahanaumokuakea marine national monument, a US conservation preserve which includes Midway atoll. The ship is said to be missing much of her flight deck, while animals have colonised her pipework and shattered metal plates.

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Historian Frank Thompson, from the naval history and heritage command in Washington, is on board the Petrel. He said: “We read about the battles, we know what happened. But when you see these wrecks on the bottom of the ocean and everything, you kind of get a feel for what the real price is for war.

“You see the damage these things took, and it’s humbling to watch some of the video of these vessels because they’re war graves.”

The massive ship – converted from a battleship hull some years before the war – was part of the six-carrier fleet that attacked Pearl Harbour in December 1941.

When the US Navy caught up with her and three other carriers six months later, she was set upon by two squadrons of Dauntless dive-bombers and suffered up to five direct hits. Fires ripped through armed and fuelled aircraft on the ship’s hangar deck, while her senior officers were killed by a strike near the bridge. She was later scuttled by torpedoes from an IJN destroyer.

Though some debris from Kaga has previously been located, this is the first time the main wreck has been spotted. More than 800 personnel from the carrier were killed at Midway.

Midway is considered a turning point in the Pacific war because Japan struggled to replace its loss of four flattops and many experienced pilots, at a time when big-gun battleships and cruisers were increasingly vulnerable to attack by carrier aircraft. By contrast, the enormous size, resources and industrial might of the US were being brought to bear.

The other three Japanese carriers sunk were the Akagi, Soryu and Hiryu, whose wrecks remain unaccounted for. The Americans lost just one, the USS Yorktown.

The Yorktown had been ordered to Midway by Admiral Chester Nimitz despite having suffered major damage at the earlier Battle of the Coral Sea. Repair teams at Pearl Harbour carried out weeks-worth of work in just two days to enable the ship to sail. She was sunk by a Japanese submarine along with the destroyer Hammann after being left dead in the water by two bombing raids, and her wreck was discovered in 1998.

The Petrel team hopes to find and survey all the wreckage from the battle, which may add new details to the history books. Earlier this year, researchers discovered the USS Hornet, an aircraft carrier that participated at Midway but was sunk in the Battle of the Santa Cruz Islands, near the Solomon Islands, just a few months later.