The company said that about 200,000 bitcoins were left in a used "wallet," the news service said. A bitcoin wallet is virtual tool that allows users to do transactions with other users.
When Mt.Gox filed for bankruptcy protection on Feb. 28 it had outstanding debts of about 6.5 billion Japanese yen ($63.5 million), 850,000 lost bitcoins and 127,000 empty-handed customers.
(Read more: Back to work at bitcoin's embattled Mt.Gox )
Mt.Gox moved the 200,000 bitcoins to an offline wallet, Kyodo News said.