Ptech, the company under investigation, has clients that include IBM, Motorola and Sprint. A statement said the company had "granted access" to investigators and is co-operating fully.
"The company categorically denies having any connection with any terrorist organisation," the statement read. "Ptech has been informed by government investigators that neither Ptech nor its officers or employees are targets of the government's investigation."
Blake Bisson, the company's vice-president of sales, said he believed federal authorities are routinely investigating companies with employees from Islamic countries. "To my knowledge, there is no link to al-Qaeda," he said.
"We are investigating the [situation] and are co-operating with authorities," said Jeffrey Gluck, a spokesman for IBM Global Services, which works with Ptech to build IT architectures for its customers. "But it's still too early in the investigation to know, with any degree of certainty, exactly what the allegations are."
Senior counterintelligence officials familiar with the case said the US Customs Service initiated the investigation of Ptech after a disgruntled employee tipped off the agency to the company's alleged hidden ownership. As a result, US Customs and the FBI began investigating Yacub Mirza, a former member of Ptech's board of directors who also manages a number of other businesses in the US.
"Mirza was acting on behalf of Yassin Qadi, the Saudi financier who was on the US [terrorism] watch list and whose accounts here are frozen," said Vince Cannistraro, the former chief of counterterrorism at the CIA. "Qadi is the guy behind Ptech."
"What this investigation shows is that the government is now paying as much attention to the role of high-tech companies in terrorism financing as they are with non-governmental organisations," said Roger Cressey, former chief of staff at the President's Critical Infrastructure Protection Board and a White House counterterrorism specialist.
A senior administration official familiar with the investigation who spoke on condition of anonymity said "a body of evidence" about the company's possible links to al-Qaeda was brought to the attention of the National Security Council months ago and triggered a government-wide investigation into where Ptech software may have been installed and, more importantly, whether malicious code was involved.
That probe has, so far, turned up no sign of malicious code, the official said.
The official added that the investigation into Ptech was not an isolated incident and that there was growing concern about terrorist financing coming out of US-based companies, including high-tech companies.