"We realize that this illicit transfer of funds from our platform and the resulting suspension in services has caused huge distress to our customers, other exchanges, and people throughout the cryptocurrency industry, and we would like to offer our deepest and humblest apologies to all of those involved", Coincheck said in a statement.
The Shibuya, Tokyo, Japan-based company said hackers broke in at 02:57am local time on Friday (12:57pm EST on Thursday, 25 January).
Yusuke Otsuka, Chief Operating Officer of Coincheck, said the stolen funds were kept in an online "hot wallet" as opposed to a much more secure offline 'cold wallet'.
The company said it would tap into its own funds to pay around 46.3 billion yen to its 260,000 customers who lost their holdings of NEM, the 10th largest cryptocurrency by market capitalization.
According to Reuters sources, Japan's Financial Services Agency sent a notice to the country's roughly 30 firms that operate virtual currency exchanges to warn of further possible cyber-attacks, urging them to step up security.
The financial watchdog is considering administrative punishment for Coincheck under the financial settlements law, a source was quoted as saying.
Late Friday evening Coincheck said it had detected unusual activity in the transfer of NEM, and immediately hurried to suspend trading on all cryptocurrencies hosted on its exchange except for Bitcoin. Asked why, CEO Wada cited technical difficulties and a shortage of staff capable of dealing with them.
The Coincheck incident marks the biggest-ever theft of digital money in the nine-year history of virtual currencies, topping the heist at Japan's Mt. Gox exchange almost four years ago.
In 2014, Tokyo-based Mt. Gox, which once handled 80 percent of the world's bitcoin trades, filed for bankruptcy after losing around half a billion dollars worth of bitcoins. More recently, South Korean cryptocurrency exchange Youbit last month shut down and filed for bankruptcy after being hacked twice a year ago.