The 32-year-old chief executive of defunct Mt. Gox pleaded not guilty to charges relating to the loss of hundreds of millions of dollars worth of bitcoins and cash from what was once the world's biggest bitcoin exchange.
French national Mark Karpeles filed the plea in response to charges of embezzlement and data manipulation at the Tokyo District Court, according to a pool report for foreign journalists.
Mt. Gox once handled 80% of the world's bitcoin trades but filed for bankruptcy in 2014 after losing some 850,000 bitcoins - then worth around half a billion U.S. dollars - and $28 million in cash from its Japanese bank accounts.
In its bankruptcy filing, Tokyo-based Mt. Gox blamed hackers for the lost bitcoins, pointing to a software security flaw.
Mt. Gox subsequently said it had found 200,000 of the missing bitcoins.
Karpeles was indicted for transferring 341 million yen ($3 million) from a Mt. Gox account holding customer funds to an account in his name during September to December 2013. He also allegedly boosted the balance of an account in his name in Mt. Gox's trading system.
Karpeles' defence had told a pre-trial consultation that the remittance was within the scope of the firm's revenue and not the embezzlement of customer funds, the Nikkei business daily reported on Tuesday.
The defence said the increased balance was part of the administrative process of exchanging cash and bitcoins and therefore not illegal, the Nikkei reported.
Karpeles told the court he was an information technology engineer.
The collapse of Mt. Gox represented a major setback for bitcoin and badly damaged the image of virtual currencies, particularly among risk-averse Japanese investors and corporations.
But the bankruptcy also prompted Japan's government to decide how to treat bitcoin, and preceded a push by local regulators to licence virtual currency exchanges.
Bitcoin can be traded on exchanges in the same manner as stocks and bonds.