The hack occurred on Friday, when the company detected an “unauthorised access” of the exchange and suspended trading for all cryptocurrencies apart from bitcoin.
The attackers were able to access the company’s NEM coins, which are a lesser known but still the world’s 10th biggest cryptocurrency by market capitalisation. The losses went up to about $534m (£380m).
The company has stated that it will reimburse the affected customers to nearly 90% of their loss using cash.
Over 260,000 are reported to have been affected by the hack.
According to Coincheck, the hackers were able to steal the NEM coins because they were kept in online “hot wallets” instead of the more secure and offline “cold wallets.”
The company claims that it is aware of the digital address where the coins have been transferred and believes the assets are recoverable.