No charges had been filed and an executive for the firm, Ptech Inc., described the raid in a broadcast interview as "routine."
ABC News first reported that U.S. Customs agents entered the Quincy, Mass., firm shortly after midnight following a six-month investigation.
The firm does business with a number of U.S. agencies, including the FBI and the Defense Department.
Customs agents downloaded files from office computers.
CNN reported that FBI agents are trying to determine whether the firm may be involved with a Middle East charity whose funds may have been diverted in the past to al Qaida, the organization which launched the Sept. 11, 2001, terror attacks.
The agents are investigating whether Ptech has a connection to Yasin al-Qadi, a Saudi businessman who is on a U.S. watch list and whose assets have been frozen because of alleged terror links, CNN said.
Employees at Ptech reacted with shock upon learning of the raid and allegations that al Qaida may have had access to super secret government files through the company and its business with government agencies.
"I doubt it at all," said Ptech employee James Cerrato. "We have government projects, but I don't think there's anything there that would be of any issue."
As to company CEO Ossama Ziade, Cerrato said he didn't believe he had ties to terrorists.
"I don't think so. He's a U.S. citizen," Cerrato said. "I've known him for a number of years."
There were no arrests connected to the raid, and the company went on with business as usual during the day.
Ziade was not immediately available for comment.
One Ptech executive, Joe Johnson, spoke to reporters outside the company's facilities in Quincy, Mass.
"Are they sympathetic to 9/11? No, I don't think so at all," Johnson said. "They are all U.S. citizens."
ABC news reported that Ptech makes software and is allegedly secretly owned by Qassin al-Kadi, one of 12 Saudi businessmen accused of funneling millions of dollars to al Qaida.
The raid, the result of a lengthy investigation by the Customs service, was coordinated by the White House amid concerns the company was secretly owned and controlled by al Qaida activists or sympathizers, ABC News said.
Details about the case reportedly were being handled by the U.S. Attorney's Office in Boston, but a call there for comment was not immediately returned.