Units of the cryptocurrency NEM worth USD 530 million were taken -- based on the exchange rate on Friday -- exceeding even the USD 480 million in bitcoin stolen from the MtGox exchange in 2014.
Coincheck suspended trading of all cryptocurrencies except bitcoin on Friday, and said it had lost 523 million units of NEM, the 10th biggest cryptocurrency in the world based on market capitalisation.
The Financial Services Agency (FSA) said in a statement that it had ordered Coincheck to investigate the cause of the incident, "properly" deal with clients, strengthen risk management and take preventive measures.
Coincheck has said it will use its own funds to reimburse about 46.3 billion yen (around $430 million) -- at a rate of 88.549 yen per NEM -- to all 260,000 customers who lost their holdings.
The company said it would reimburse customers in yen, not cryptocurrency.
The FSA said at a briefing Monday that it was checking to ensure Coincheck had the ability to make those refunds.
The watchdog added that it was carrying out checks at other exchanges in the wake of the theft to detect potential security problems.
"While examining the cause of the incident and taking necessary measures, we want the ministries and agencies concerned to urgently study what further measures we'd need," the top government spokesman said.
Japan's Finance Minister Taro Aso told parliament on Monday that the government would take "necessary administrative measures, including an on-site inspection."
Coincheck "did not store the important things separately. I think they lacked fundamental knowledge or common sense," he said.
One unit of NEM was trading at 95 cents at around 0730 GMT on Monday, according to coinmarketcap.com.
As many as 10,000 businesses in Japan are thought to accept bitcoin, and bitFlyer -- the country's main bitcoin exchange -- saw its user base grow beyond one million in November.
Many Japanese, especially younger investors, have been seduced by the idea of strong profits as the economy has seen years of ultra-low interest rates offering little in the way of traditional returns.
In the wake of the MtGox scandal, Japan passed a law on cryptocurrencies that requires exchanges to be regulated by the FSA.
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