Police are also liaising with relevant partner agencies in New Zealand and overseas.
The investigation is still in its very early stages.
Cryptopia posted on Twitter to alert users that on January 14 it had "suffered a security breach which resulted in significant losses".
"Once identified by staff, the exchange was put into maintenance while we assessed damages," it wrote.
"Staff then notified and involved the appropriate Government Agencies, including NZ Police and High Tech Crimes Unit who are jointly and actively investigating the matter as a major crime and they are assisting us with advice."
The company said that until this is carried out, the Cryptopia Exchange would remain in maintenance mode, with trading suspended.
"We are committed to getting this resolved as quickly as possible."