The FBI wanted to arrest Kashmiri separatist leader Ghulam Nabi Fai several times earlier this year but did not do so following directions from the US State Department or the CIA as they feared it may further strain already frayed ties with Pakistan.
The FBI arrested 62-year-old Fai, a US citizen, on July 19 on charges of being an ISI agent who lobbied for the the Pakistani spy agency and army on the Kashmir issue in America.
The agency filed a 43-page affidavit in a US court in connection with the indictment of Fai and another US citizen Zaheer Ahmad, 63, as agents of Pakistan.
The FBI had originally hoped to arrest the two men working for the charity -- the Kashmiri American Council --several times earlier this year but was told each time by the State Department or the CIA that the arrests would only aggravate the frayed relations between the US and Pakistan, The New York Times reported quoting an unnamed American security official.
The indictments came as the CIA was trying to negotiate the release of a Pakistani doctor who was jailed by the ISI on accusations that he had helped the Americans track down al-Qaeda chief Osama bin Laden before his killing in Abbottabad near Islamabad.
A senior official at Pakistan's Embassy in Washington, speaking on the condition of anonymity, said it was customary for intelligence agencies to operate "outside the limelight," adding that it was unfortunate that the ISI had become a subject of "demonisation."
"There is nothing that the ISI does in the United States that is not part of the normal function of intelligence agencies," the embassy official said. "The ISI has never deliberately violated an understanding with the US government or deliberately violated American law."