By Agence France-Presse
Osaka-based Tech Bureau, which operates virtual currency exchange Zaif, said its server had been illegally accessed and money transfered.
"We decline to comment on the details of how this illegal access occurred, as it is a crime and we've already asked the authorities to investigate," Tech Bureau said in a statement.
It added that the virtual currencies stolen were bitcoin, monacoin, and bitcoin cash.
"We will prepare measures so that customers' assets will not be affected" by the hack, it said, adding it would receive financial support from major shareholder Fisco Group.
Japan is a major centre for virtual currencies and as many as 50,000 shops in the country are thought to accept bitcoin.
Earlier this year, Japan-based exchange Coincheck suspended deposits and withdrawal for virtual currencies after it had been hacked, resulting in a loss worth half a billion US dollars of NEM, the 10th biggest cryptocurrency by market capitalisation.
Japanese authorities later ordered two cryptocurrency exchanges to suspend operations as part of a clampdown following the hack.