The company is also considering preventative measures and compensation For customers, through specific details were not revealed.
Coincheck has alerted Tokyo police to the theft.
According to its website, which proclaims it is "the leading bitcoin and cryptocurrency exchange in Asia", Tokyo-based Coincheck was founded in 2012 and had 71 employees as of July a year ago.
According to Coincheck, the company's outstanding balance in NEM was found to have decreased dramatically on the morning of January 26.
Coincheck announced in an that it had stopped trading of NEM and other coins as it dealt with the hack.
Sales and withdrawals of the currency were halted after the company became aware of the situation, over 8 hours after the incident.
The exchange is now investigating how many customers were impacted by the hack, and has said it is considering possible responses, including compensation for those whose NEM was taken.
Experts say it is common for virtual currency exchanges to store currencies in systems that are shut off from outside networks to prevent outsiders from illegally accessing the systems. Some reports suggest that NEM might not be the only currency missing.
NEM, the 10th-largest cryptocurrency by market value, fell 14 per cent to 81 U.S. cents in the 24 hours through 10:07am.
Both bitcoin and NEM tumbled after the news broke.
Not surprisingly, investors were anxious.
On Friday night, users of Coincheck had gathered around the building in central Tokyo where it is located. His investment is now valued at about 500,000 yen. "I am beside myself with worry right now". Another said, "Can I take back my money?" "I think there are things they could have done inside the company to prevent trouble like this".
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