Mark Karpeles, 30, is being held regarding the loss of bitcoins worth $387m (£247m, €351m) last February.
He is associated with having gotten to the trade's PC framework to misrepresent information on its exceptional parity.
MtGox asserted it was brought on by a bug yet it later petitioned for insolvency.
Japan's Kyodo News said a legal counselor following up for Mr Karpeles' sake denied his customer had done anything unlawful.
Mr Karpeles, who was conceived in France, is associated with profiting to the tune of $1m (£640,000), the office said.
In Walk 2014, a month in the wake of petitioning for insolvency, MtGox said it had discovered 200,000 lost bitcoins.
The firm said it discovered the bitcoins - worth around $116m - in an old advanced wallet from 2011.
That brings the aggregate number of bitcoins the firm lost down to 650,000 from 850,000.
That aggregate sums to around 7% of all the bitcoins in presence.
Bitcoin is a virtual cash assembled around a confounded cryptographic convention and a worldwide system of PCs that administers and checks which coins have been spent by whom.