In response to requests from the families of Ehime Maru's victims and the government of Japan, the USN raised Ehime Maru from the ocean floor during October 2001 and moved it to shallow water closer to Oahu.
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Using the Phoenix III ROV, contractors, beginning on 20 July 2001, first removed Ehime Maru's mast and other items on the ship's decks that could interfere with the lifting operation. Assisted by technical experts from Japan, including one from the company that built Ehime Maru, the Rockwater II contract diving support vessel prepared the ship for lifting beginning the first week of August. After some difficulty, Ehime Maru was lifted off the ocean floor by Rockwater II on 5 October and moved slowly to a location closer to shore. On 14 October the wreck was set down in 115 ft (35 m) of water one statute mile (1.6 km) south of Honolulu International Airport's reef runway.[65]
On 15 October, the first team of USN divers from Mobile Diving and Salvage Unit ONE (MDSU-1) began assessing the sunken vessel. Working in low- to zero-visibility conditions, 66 MDSU-1 and 30 Japanese JMSDF divers from the submarine rescue ship JS Chihaya conducted 526 dives over 29 days, searching the wreck.
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After the recovery was complete, on 25 November, Ehime Maru was lifted, towed back out to sea suspended about 90 feet (27 m) below the towing barge, and scuttled in 6,000 feet (1,800 m) of water 12 nautical miles (22 km) south of Barbers Point.[67][68] The event was witnessed by three of Ehime Maru's victims' families on board Chihaya. The total cost of the salvage operations was about $60 million.