Japan-based virtual currency exchange Coincheck said Sunday it will refund about $400 million to customers after hackers stole hundreds of millions of dollars' worth of digital assets.

The company said it will use its own funds to reimburse about 46.3 billion yen to all 260,000 customers who lost their holdings of NEM, the 10th biggest cryptocurrency by market capitalisation.

On Friday, the company detected an "unauthorised access" of the exchange, and later suspended trading for all cryptocurrencies apart from bitcoin.

The resulting 58 billion yen ($530 million) loss exceeded the value of bitcoins which disappeared from MtGox in 2014.