The attack was going on for eight weeks and BAE was called in by the fund at the end of 2013, said Paul Henninger, global product director for BAE Systems Applied Intelligence. He said it had "all the signatures of an organized crime attack."

"This is the first time we've seen criminals actively go after a business system and effectively take over that system and create sabotage," Henninger said in a phone interview. "The assumption is that this was a for-profit attack."

The hackers inserted malicious software that delayed by several hundred microseconds the ability to trade, said Henninger, who declined to identify the hedge fund or its location. The target was the fund's order entry system, he said.

"The difference in a few microseconds can mean a significant difference in the profitability of that trade," Henninger said.

CNBC reported about the hacking earlier today.