Coincheck froze deposits and withdrawals for all crypto-currencies except Bitcoin as it assessed its losses in NEM, a lesser-known currency.
It may be unable to reimburse the funds lost on Friday, a representative told Japanese media.
If the theft is confirmed, it will be the largest involving digital currency.
Another Tokyo exchange, MtGox, collapsed in 2014 after admitting that $400m had been stolen from its network.
The stolen Coincheck assets were said to be kept in a “hot wallet” – a part of the exchange connected to the internet. That contrasts with a cold wallet, where funds are stored securely offline.
Coincheck says it has the digital address of where the assets were sent.
Hackers broke in at 02:57 on Friday (17:57 GMT Thursday), the company said in a statement, but the breach was not discovered until 11:25, nearly eight and a half hours later.
Company chief operating officer Yusuke Otsuka said 523m NEMs had been sent from Coincheck’s NEM address during the breach.
“It’s worth 58bn yen based on the calculation at the rate when detected,” he told reporters at the Tokyo Stock Exchange.
Coincheck was still examining how many customers had been affected and trying to establish whether the break-in had been launched from Japan or another country.
“We know where the funds were sent,” Mr Otsuka added. “We are tracing them and if we’re able to continue tracking, it may be possible to recover them.”
Coincheck reported the incident to the police and to Japan’s Financial Services Agency. (Courtesy BBC)