Mt Gox, once the world's biggest bitcoin exchange, has filed for bankruptcy protection in Japan.
It said it may have lost nearly $500 million worth of the virtual coins due to hacking into its faulty computer system.
The collapse caps a tumultuous few weeks in which the company has remained virtually silent after halting trades of the virtual currency, shaking the nascent but burgeoning bitcoin community.
Wearing a suit instead of his customary T-shirt, Mt Gox's French CEO Mark Karpeles bowed in contrition and apologised in Japanese at a news conference at the Tokyo District Court.
He blamed his firm's collapse on a "weakness in our system", but predicted that bitcoin would continue to grow.
"First of all, I'm very sorry," he said. "The bitcoin industry is healthy and it is growing. It will continue, and reducing the impact is the most important point."
Angry investors have been seeking answers for what happened to their holdings of cash and bitcoins on the unregulated Tokyo-based exchange.
Mt. Gox said the exchange, used overwhelmingly by foreigners, had lost 750,000 of its users' bitcoins and 100,000 of its own. At the current bitcoin price of about $565, that would total some $480m - representing about 7% of the estimated global total of bitcoins.
It also said there was a discrepancy of 2.8 billion yen ($27.4 million) in its bank accounts when it checked on Monday.
Many bitcoin market participants have said Mt Gox's problems were specific to the company and were caused by what they said was a lax attitude by Karpeles, while bitcoin itself - free of any central bank control - was still a noble venture.
"If we could agree on legal regulation, we should let (bitcoin and regulators) co-exist," said Keiichi Hida, a bitcoin investor and member of the Japan Digital Money Association. He lost about 100,000 yen worth of bitcoins, but seemed unconcerned as he became interested in the virtual currency as a form of "study".
"We should make it a national project to have bitcoin used nationwide at the time of the 2020 Tokyo Olympics," he said.
Mt Gox deleted its website on Tuesday after freezing withdrawals earlier this month in the wake of a series of technical difficulties.
The exchange had liabilities of 6.5 billion yen ($63.67m), dwarfing its total assets of 3.84 billion yen, the company said. It had 127,000 creditors in bankruptcy, just over 1,000 of whom are Japanese.
The company and Karpeles have said little in the days before today's court filing, which is similar to Chapter 11 bankruptcy in the US, except that they were working with others to resolve their problems.
Another lawyer said Mt Gox wanted to file a criminal complaint against what he said was a hacking attack, but had no specific means of doing so.