MTGox's shut down prompted some bitcoin traders to picket the exchange's offices
The application was made in Japan by lawyers acting on behalf of the exchange and comes only days after MtGox went offline.
The application was made in Japan by lawyers acting on behalf of the exchange and comes only days after MtGox went offline.
On Tuesday, the exchange's boss said he was working hard to find a "solution to our recent issues".
Before going offline, technical troubles meant it prevented customers transferring digital cash to other exchanges on 7 February.
Details of the bankruptcy are scant but the application for protection has been accepted by a district court in Tokyo, reported AFP. At the court hearing, the company said it had outstanding debts of about 6.5bn yen (£38m).
MtGox's lawyers are believed to have decided to apply to the court for protection after US regulators filed a subpoena against the company.
Reports suggested the site shut down after it discovered that an estimated 744,000 bitcoins - about $350m (£210m) - had been stolen due to a loophole in its security.
MtGox's troubles have put pressure on the price bitcoin owners can get for their holdings. Currently one bitcoin is worth about $561 (£334), a price far lower than the high of $1,000 per coin it hit in November 2013.
Meanwhile, Vietnam has banned its banks from from handling the crypto-currency saying the virtual cash is not legal tender. The country's state bank said trading in bitcoins carried "potential risks" for users.
At the same time, Japan's deputy finance minister said any regulation of bitcoin would have to involve international cooperation to avoid opening up loopholes that traders could exploit.
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