Robin Raphel, 67, considered one of the leading American experts on Pakistan, was placed under federal counter intelligence investigation earlier this month.
The telephone conversation led to months of secret surveillance on her and during an FBI raid at her home last month agents discovered classified information, a report in the New York Times said, describing the investigation as a "rare example" of a FBI espionage investigation breaking into public view.
FBI agents searched her home in a prosperous neighbourhood near the Maryland border with Washington and found classified information, the officials said.
Raphel was stripped of her security clearances last month and no longer has access to the State Department building.
Raphel has not been charged with a crime and it is still unclear what the Pakistani official said in the intercepted conversation that led to the investigation against Raphel.
With new details shedding light on the evidence in the case, Justice Department prosecutors are weighing whether to bring charges against Raphel, who rose to become one of the highest-ranking female diplomats and a fixture in foreign policy circles, serving as ambassador to Tunisia and as assistant secretary of state for South Asian affairs in the Clinton administration.
After retiring from the government in 2005, she lobbied on behalf of the Pakistani government before accepting a contract to work as a State Department advisor.
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