The exchange's CEO Mark Karpeles appeared before Japanese TV news cameras Friday, bowing deeply for several minutes.
He said a weakness in the exchange's systems was behind the massive loss of the virtual currency.
Speaking in Japanese at a Tokyo court, he apologized for the troubles he had caused so many people.
Kyodo News said debts at Mt. Gox totaled more than 6.5 billion yen ($65 million), surpassing its assets.
The exchange's unplugging this week drew renewed regulatory attention to a currency created in 2009 as a way to make transactions across borders without third parties such as banks.