MtGox filed for bankruptcy in Japan on Friday. It came after the site had closed down after losing an estimated 750,000 of its customers' bitcoins.
"Illegal access through the abuse of a bug in the bitcoin system" meant a "high probability" the bitcoins had been stolen, it said in a statement.
Investigations are under way, it added.
Much of the statement released on MtGox's website confirmed details contained in a leaked document that surfaced just days before the bankruptcy application.'Crimes punished'
As well as the 750,000 customers' bitcoins that were lost, the company also said it had lost approximately 100,000 of its own. This amounts to nearly $500m (£300m).
It also said MtGox accounts held with financial institutions currently held approximately 2.8bn yen (£16.5m) less than the amount MtGox users had deposited.The value of Bitcoin has suffered with the closure of MtGox
To "establish the truth" about what had happened a "huge amount of transaction reports" would need to be investigated, the statement said. Because of this MtGox could not give an exact amount of missing deposit funds or the total amount of bitcoins that had disappeared.
MtGox also said that it had appointed an expert to look at the possibility of criminal proceedings.
"We will make all efforts to ensure that crimes are punished and damages are recovered," it said.
The possibility of continuing as a business in order to pay back creditors was also being explored, the company said.
A call centre has also been set up answer customers questions.
Japan said on Tuesday that the government was still trying to determine what had led to the collapse of MtGox.
"We still have not had a clear grasp of the situation," Japanese Finance Minister Taro Aso said according to Reuters. "[We] don't know if it was a crime or just theft."