A counterterrorism program that was gutted in 2012 may have been able to thwart the terrorist attack in San Bernardino, Calif., according to a former Department of Homeland Security (DHS) employee.

Phillip Haney said that during his work on the Intelligence Review Unit (IRU) at DHS, he flagged the Redlands, Ca., mosque that was attended by Syed Farook, one of the two shooters in California. Haney said the program would have likely singled out Farook and prevented him from bringing the other shooter, his fiancée Tashfeen Malik, into the country on a K-1 visa.

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“I can tell you how I would have identified it, because individuals that were already in the case in 2012 went to that mosque,” Haney said Thursday night on Fox News’s “The Kelly File.” “Therefore, as we were tracking them, we would have put the red light on them."

“Therefore, two things very plausibly would have happened: Either Syed would have been put on the no-fly list because of his association with that mosque, and/or the K-1 visa that his wife was given may have been denied because of his affiliation with a known organization,” he added.

Farook traveled to Saudi Arabia to marry Malik in 2012 and later brought her to the U.S. through the visa.

Haney, a founding DHS member, said the program was shut down in 2012 by the State Department and the DHS Office for Civil Rights and Civil Liberties because it profiled Islamic groups.

He said he filed a Freedom of Information Act (FOIA) request in order to find out why the program had been ended.

“They specifically said that because we FOIA'd the case, and we got the internal memos, and it says that we are not allowed to develop a case based on … any Islamic group,” he said.

Haney said the program had tracked the movements of people affiliated with suspected terrorist organizations.

“We had thousands of organizations or individuals in the database, and we tracked them as they moved in and out of the United States on the Visa Waiver Program — that’s what first brought the group to our attention,” he said. “And as we developed the case and started putting pieces in place, we gained more and more evidence of their activities.”

Haney told the Federalist on Friday that, because Islamic groups being tracked by his program were not on the Specifically Designated Terrorist Organizations list, tracking individuals affiliated with the groups was considered a violation of their civil liberties.

“The administration was more concerned about the civil liberties of foreign Islamic groups with terrorist ties than the safety and security of Americans,” he said.

The DHS told Fox News that there are "many holes" in Haney’s story but refused to comment further on the report due to privacy laws.

Law enforcement official say Farook and Malik killed 14 and injured 21 when they attacked the San Bernardino Regional Inland Center on Dec. 2.

Malik pledged her allegiance to the Islamic State in Iraq and Syria (ISIS) in a social media post at the time of the attack.