The company said it used its own funds to reimburse about 46.6 billion yen ($440 million) to all 260,000 customers who lost their holdings of NEM, a leading cryptocurrency.
"Procedures have been completed with the accounts of all 260,000 customers," company spokesman Yosuke Imai told AFP.
Thieves syphoned away 523 million units of the cryptocurrency from Coincheck -- then valued at $547 million -- during the January 26 hack, which exceeded the $480 million in bitcoin stolen in 2014 from another Japanese exchange, MtGox.
Authorities raided Coincheck's office last month and have slapped the company with sanctions.
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The firm had failed to upgrade its systems to keep up with the rapid expansion of the cryptocurrency market, he said.
In February, seven plaintiffs -- two companies and five individuals -- filed a lawsuit against Coincheck seeking the reimbursement of 19.53 million yen in lost virtual currency and further compensation for interest lost due to the hack.
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