Foreign Office spokesperson Tasnim Aslam said the impression that Robin Raphel, 67, was interrogated because she was a friend of Pakistan was incorrect.
"Robin Raphel has had a long association with Pakistan and with this region and she is someone who understands this region. As regards, the investigation, that is an internal US matter," she said.
Aslam said Pakistan has neither asked the US to share the investigation nor has the US disclosed the reason for probing her.
Raphel was seen as a brazenly pro-Pakistan partisan in Washington. She is one of the highest ranking former female diplomats in the US to be the subject of an FBI investigation.
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The FBI has searched her residence and sealed her office on charges of taking classified information home from the State Department.
Till early this month Raphel was a senior advisor to the State Department on civilian aid to Pakistan.
After her retirement, she had returned to the private sector and worked as a lobbyist for Pakistan.