The exchange, Bitfinex, reported the intrusion on Tuesday and said it was working with law enforcement.
“We are investigating the breach to determine what happened, but we know that some of our users have had their bitcoins stolen,” the exchange said.
Its statement doesn't say how many bitcoins are missing, but Zane Tackett, the site's director of community and product development, said on Reddit that the losses stand at 119,756 bitcoins. Bitfinex didn't immediately respond to a request to confirm that figure.
A bitcoin was trading at $527.25 at the time of this report, although the price was falling as news of the hack spread.
Bitfinex is used to trade other digital currencies too, including ether and litecoin, but the site says only bitcoins were affected.
“As we account for individualized customer losses, we may need to settle open margin positions, associated financing, and/or collateral affected by the breach,” the exchange said.
“We will look at various options to address customer losses later in the investigation.”
It's not the first exchange to have lost money in a breach this year. In April, Shapeshift was hacked in what it said later was an inside job. A month later, Gatecoin was reportedly hacked to the tune of about $2 million.
Those incidents were dwarfed by the collapse of Tokyo-based Mt. Gox two years ago, which shut down after losing bitcoins valued then at $474 million.
"We are going to keep the site down until we are 100 percent certain that the site is secure and that is safe to bring everything back online," Tackett said Tuesday on Reddit, where he was frantically answering questions from users.