U.S. Pakistan expert loses security clearance in federal probe WASHINGTON (Reuters) - A U.S. State Department expert on Pakistan was stripped of her security clearance and is part of a federal counterintelligence investigation, two sources familiar with the matter said on Friday. Robin Raphel, a retired ambassador who had been an adviser to the State Department's Special Representative for Afghanistan and Pakistan (SRAP), had her house searched about three weeks ago, said a law enforcement source who asked not to be named. Her security clearance was revoked before her contract was allowed to expire, said a second source who also spoke on condition of anonymity. She is a career diplomat who has served as ambassador to Tunisia and assistant secretary of state for South and Central Asia. The Washington Post newspaper first reported Raphel's case. The exact nature of the investigation remained unclear but the Post cited two U.S. officials as saying it was a counterintelligence matter, which usually involves spying allegations. Raphel retired from the State Department and then returned in 2009 as a contract employee at the U.S. embassy in Islamabad and later at the State Department's key policy-making office on Pakistan. The second source said Raphel oversaw all U.S. development and civilian aid to Pakistan when she worked on a contract in Islamabad. On returning to Washington, she continued to focus on civilian assistance and building economic ties with Pakistan. The Post said the FBI searched Raphel's Washington home on Oct. 21, removing bags and boxes, and also searched her State Department office. She was placed on administrative leave last month and her contract with the State Department was allowed to expire this week, the paper said. The newspaper cited a spokesman for Raphel as saying she had not been told that she was a target of the probe but that she was cooperating. No charges have been filed. Asked about the Post report, State Department spokeswoman Jen Psaki said: "We are aware of this law enforcement matter. The State Department has been cooperating with our law enforcement colleagues on this matter. "Ms. Raphel's appointment expired; she is no longer a Department employee," the spokeswoman said. Raphel's ex-husband, Arnold Raphel, was the U.S. ambassador to Pakistan in 1988 when he died in a plane crash that also killed Pakistani President Mohammed Zia ul Haq. There have long been suspicions that the crash may have been caused by sabotage. Reporting by Mark Hosenball, Arshad Mohammed and Bill Trott; Editing by David Storey and Bernadette Baum