A Japanese virtual currency exchange which lost some 58 billion yen ($534 million) of its customers' holdings may be unable to offer to reimburse the lost funds, a representative of the exchange operator said Saturday.

In one of the largest losses of cryptocurrency resulting from a hacking event, nearly all of the NEM currency held by the Tokyo-based exchange Coincheck disappeared early Friday.

While the exchange has not disclosed the size of its asset base, the representative said, "In the worst case scenario, we may not be able to return clients' assets."

Coincheck has said it detected a party gaining unauthorized access to its system shortly before 3 a.m. Friday.

In response, it suspended the deposit, withdrawal, sales and purchase of NEM as well as the withdrawal of the other cryptocurrencies and Japanese yen it holds.

Coincheck President Koichiro Wada said in a press conference late Friday its NEM accounts are managed on a system accessible by the internet, but the exchange believes it took all possible security precautions.

Wada said the company has not been able to complete development of its technology allowing the management of virtual currencies offline due to technical difficulties and a shortage of technicians.

Other cryptocurrency exchanges in Japan were operating normally Saturday morning.

The latest theft is the largest since the Mt. Gox bitcoin exchange in Tokyo lost 48 billion yen in 2014.