On Sunday, major newspapers in the country labelled the management of virtual currencies at Coincheck as sloppy and said the company had expanded business by putting safety second.
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On Friday, the company detected an unauthorised access of the exchange and later suspended trading for all cryptocurrencies apart from bitcoin.
Pre-existing operators such as Coincheck have been allowed to continue offering services while awaiting approval. Coinchecks application, submitted in September, is pending.
The Tokyo-based bitcoin exchange collapsed after admitting that 850,000 coins, worth around $480m at the time, had disappeared from its vaults.
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Politicians meeting last week at theWorld Economic Forum in Davosissued warningsabout the dangers of cryptocurrencies, with the US Treasury secretary, Steven Mnuchin, relating Washingtons concern about them being used for illegal activity.
Coincheck said it would use its cash to reimburse about 46.3bn yen to the 260,000 people who lost their holdings of NEM, the worlds 10th-biggest cryptocurrency by market capitalisation.
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The resulting 58bn yen loss exceeded the value of bitcoin thatdisappeared from MtGox in 2014.
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MtGoxs high-profile demise failed to dampen the enthusiasm for virtual currencies in Japan, which became the first country todefine cryptocurrencies as legal tenderin April last year.
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A Japan-based cryptocurrency exchange will refund to customers about $400m (282m) stolen by hackers two days ago in one of the biggest thefts of digital funds.
From VR porn to Kidcoin: inside the cryptocurrency trade fair
Coincheck will reimburse 260,000 customers who lost holdings of NEM currency
Local media said the Financial Services Agency was expected to take action against Coincheck, which calls itself the leading bitcoin and cryptocurrency exchange in Asia.
Sun 28 Jan 201809.04 GMTLast modified on Mon 29 Jan 201819.04 GMT
As many as 10,000 businesses inJapanare thought to accept bitcoin, and bitFlyer, the countrys main bitcoin exchange, saw its user base pass the 1 million mark in November.
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Bitcoin is based on the blockchain pipe dream
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Coincheck said its NEM coins were stored in a hot wallet instead of the more secure cold wallet, which is kept offline, because of technical difficulties and a shortage of staff capable of dealing with them.
Japan started to require cryptocurrency exchange operators to register with the government last April.
Nearly one-third of global bitcoin transactions were denominated in yen last month, according to the specialist .
Many Japanese people, 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.
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