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A Senate committee has subpoenaed San Diego FBI agents in its investigation of whether the government mishandled information about the alleged Fort Hood shooter prior to the deadly November attack, but the Justice Department’s defiance has prompted the committee to issue new threats.

In a sharply worded letter to Attorney General Eric Holder and Defense Secretary Robert Gates yesterday, the Senate Homeland Security and Governmental Affairs Committee slammed the departments for stonewalling and threatened to find the top officials in contempt of Congress if they don’t comply with subpoenas by June 2.

The committee is trying to evaluate, among other things, the FBI’s actions when it intercepted e-mails indicating that Army Maj. Nidal Hasan, accused of murdering 13 military colleagues in a shooting rampage at the Texas military base, was communicating with former San Diego Muslim leader Anwar al-Awlaki, now a target for CIA assassination.

“Without the direct testimony of these agents, the committee cannot discharge its investigation’s primary task: ascertaining what the U.S. government knew and what actions it took concerning Major Hasan before the attack,” said the letter, signed by committee chairman, Sen. Joe Lieberman and ranking member Sen. Susan Collins.

The San Diego FBI’s Joint Terrorism Task Force had obtained numerous e-mails between Hasan and Awlaki, once a charismatic leader of a local mosque and spiritual advisor to San Diego-based Sept. 11 hijackers.

Awlaki, an American citizen, was first thought to be a peace-promoting moderate, but has since left the country and become so radical he recently called on Muslims to murder American civilians, and the White House in April approved Awlaki for a CIA list of targets for assassination. He is also said to have inspired the suspect charged with the recent failed Times Square bombing, Faisal Shahzad.

Two local federal law enforcement sources have said the San Diego FBI warned counterparts in Washington, D.C., about the communications between the two men before the shooting, but their concerns were not heeded.

So far, the FBI has refused to make the agents available for interviews, but it has turned over to the committee classified e-mails between Hasan and Awlaki, as well as exchanges within the FBI’s Joint Terrorism Task Forces in San Diego and Washington, D.C., and headquarters, about the Hasan-Awlaki liaison, according to correspondence posted on the committee’s website. A committee spokesman declined to discuss the nature of the e-mails.

In letters responding to the committee, top attorneys for the Justice Department and the Pentagon said they had already turned over about 1,000 pages of documents and briefed committee staffers. They have said that offering up agents for interviews would jeopardize Hasan’s criminal prosecution.

The committee has argued that it’s not investigating the criminal aspect of the case, but whether the government dropped the ball before the crime happened, and if so, how that can be prevented in the future.

FBI officials in San Diego and Washington declined to comment on the subpoenas or the latest letter. A Justice Department spokeswoman couldn’t immediately be reached for comment.

The Senate committee has interviewed at least one San Diego-based federal agent, Ray Fournier, who was a member of the local Joint Terrorism Task Force during the investigation of the Sept. 11, 2001, and who investigated and tried to build a passport fraud case against Awlaki.

He said the committee interviewed him last month for about 20 minutes, focusing mostly on what he knew about the relationship between the San Diego and Washington, D.C. task forces.

“It was clear that they’re trying to figure out why they’re being stonewalled by various government agencies on these e-mails about Awlaki’s interaction with Maj. Nadal Hassan,” said Fournier, formerly an agent with the State Department.

Committee staff members asked Fournier if the terrorism task forces in San Diego and Washington were “in sync.” “I’ve got to answer no to that,” Fournier said. “FBI headquarters does whatever the hell they want to do, and they don’t necessarily communicate well out in the field. The Anwar Awlaki story pinpoints this.”

Fournier explained that in the weeks after the Sept. 11 attacks, he and fellow San Diego agents were desperately trying to build a passport fraud case against Awlaki — anything to get him into custody, because they believed he was a serious threat. Awlaki was indicted, but headquarters was not on board.

Charges were filed and an arrest warrant was issued for Awlaki, whose name has also been spelled “al-Aulaqi,” on June 17, 2002, by a magistrate judge in Denver, for felony passport fraud. But three months later, prosecutors decided they didn’t have enough evidence to support a conviction and went to the judge and had the warrant rescinded.

At the same time, Fournier said, Washington was apparently working at cross purposes, trying to get an arrest warrant thrown out so they could either recruit Awlaki as an informant, or let him go free and follow him around and see what he did.

FBI headquarters disputed that characterization today. “The passport fraud didn’t go forward because prosecutors within the jurisdiction decided there was not enough to sustain a prosecution — pure and simple,” said FBI spokesman Jason Pack. He declined further comment.

Fournier has not been part of the San Diego task force for several years and was not privy to information about communications between Hasan and Awlaki.

The San Diego agents had been monitoring Awlaki since he came to their attention after the terrorist attacks. In the Fort Hood matter, the agents had tracked the communication between the two from December 2008 to the middle of this year, federal sources said.

Contact Kelly Thornton directly at kellythornton7407@yahoo.com. And follow her on Twitter @kellymthornton.

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