The Maritime Self-Defence Force was using the remote-controlled submersible in the Tsugaru strait between Japan's main island of Honshu and its northern landmass, Hokkaido, in November, a defence ministry official said.
"The vehicle was being used to survey the underwater terrain as well as water currents and temperatures," he told AFP.
The unmanned craft, which is three metres (10 feet) long and two metres wide, and weighs about five tons, disappeared after the cable that connected it to a surface ship was severed.
"The ministry has set up a panel to investigate how it was lost," said the official.
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