The indictment of France-born Mark Karpeles, 30, comes after he was taken into police custody in Tokyo last month over the affair. He remained in custody today but has the option of petitioning the court for release pending trial.
The charges are tied to allegations that Karpeles falsified data while another relates to claims he pocketed millions of dollars of Bitcoin deposits.
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Karpeles was first taken into custody over claims he fraudulently tinkered with data and transferred funds to other firms controlled by him dozens of times between 2011 and 2013.
He was later rearrested for allegedly pocketing about 321 million yen ($2.7 million) worth of Bitcoin deposits, extending an initial three-week incarceration during which time police likely grilled him over the incident.
Bitcoins are generated by complex chains of interactions among a huge network of computers around the planet, and are not backed by any government or central bank, unlike traditional currencies.
Tokyo-based MtGox shuttered last year after admitting 850,000 coins -- worth around $480 million at the time, or $387 million at current exchange rates -- had disappeared from its digital vaults.
The exchange, which once said it handled around 80 per cent of global Bitcoin transactions, filed for bankruptcy protection soon after the cyber-money went missing, leaving a trail of angry investors calling for answers.
The company initially said there was a bug in the software underpinning Bitcoins that allowed hackers to pilfer them.
Karpeles later claimed he had found some 200,000 of the lost coins in a "cold wallet" -- a storage device, such as a memory stick, that is not connected to other computers.
But the whereabouts of the money and Karpeles' involvement appear far from solved.
"I'm happy the police have made breakthroughs on investigating the missing fiat money, but it would be unsatisfying if after all this time all we get is a conviction for manipulated records and embezzlement only amounting to a fraction of all the money people lost," Bitcoin investor Kim Nilsson told AFP.
"It may be better than nothing for the people who want to see someone held responsible, but I think we should be expecting more.
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