WASHINGTON (Reuters) - A State Department expert on Pakistan was stripped of her security clearance and is part of a federal counterintelligence investigation, the Washington Post reported on Friday.

The FBI searched the Washington home of Robin L. Raphel on Oct 21, removing bags and boxes, as well as her State Department office, the Post said. She was placed on administrative leave last month and her contract with the State Department was allowed to expire this week, the Post said.

The exact nature of the investigation remained unclear but the Post cited two US officials as saying it was a counterintelligence matter, which usually involves spying allegations.

The newspaper quoted 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.

A State Department spokeswoman acknowledged the investigation but declined further comment, the Post said. Raphel did not respond to the Post's requests for comment.

The newspaper said Raphel, 67, was a senior adviser on Pakistan for the State Department in a job responsible for administering non-military aid, such as economic grants and incentives.

She previously had worked as assistant secretary for South and Central Asian affairs and ambassador to Tunisia, along with postings in South Africa, Britain and India. She retired from the State Department in 2005 and returned four years later as a contract employee, the Post said.

Raphel's ex-husband, Arnold Raphel was the US ambassador to Pakistan in 1988 when he died in a plane crash that also killed Pakistani President Mohammed Zia ul Haq and was believed to have been caused by sabotage.