Tech Bureau, the operator of Japanese cryptocurrency exchange Zaif, reported on Thursday morning that hackers had stolen 6.7 billion yen ($60 million) worth of digital currencies.
Of the amount stolen, about 4.5 billion yen belonged to exchange customers.
The exchange was hacked on Sept 14. Three types of digital coins -- Bitcoin, Bitcoin Cash and Monacoin -- were stolen from "hot wallets," which are connected to networks at all times.
The company did not detect the hack until Sept. 17, after which the exchange immediately stopped all transactions. Tech Bureau confirmed the hack on Sept. 18, reporting it to the Financial Services Agency and investigative authorities.
Tech Bureau will sell a majority of its shares to a group company under financial services provider Fisco, in order to compensate customers.
In January, Japan's cryptocurrency markets were rocked when Coincheck lost 58 billion yen worth of NEM digital currency in a hack, which also targeted hot wallets.