The hack of Coincheck was one of the largest of its kind, and prompted authorities to search the firm's offices last week, after slapping it with an administrative order.
Finance Minister Taro Aso said on Friday those raids were now being expanded.
"We have started to raid several virtual currency exchanges," he told reporters, adding that the raids were intended to "examine their internal governance structure".
Aso, also the minister in charge of financial services, has admitted that the government "needs to strengthen our supervision" of virtual currency exchanges.
In the wake of the theft, the country's Financial Services Agency instructed more than a dozen local exchanges to submit reports on their efforts to monitor systemic risks.
Thieves syphoned away 523 million units of the cryptocurrency NEM from Coincheck during the January 26 hack, exceeding the USD 480 million in virtually currency stolen in 2014 from another Japanese exchange, MtGox.
That hack prompted Japan to issue new regulations, requiring exchanges to obtain a licence from the FSA, but Coincheck was allowed to continue operating while the agency was reviewing its application.
Reports in Japan's media in recent days have suggested hackers may have accessed the firm from abroad.
The Yomiuri Shimbun earlier this week cited unnamed police sources as saying Coincheck was repeatedly accessed illegally through servers in the United States, Germany and the Netherlands in the days before it was hit.
And the Asahi Shimbun daily reported Friday that part of the stolen cryptocurrency was sent to an exchange in New Zealand called Cryptopia.
Cryptopia offers a platform for trading various virtual currencies including bitcoin, according to its website.
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