Speaking at a press conference on Wednesday with Afghan President Hamid Karzai, Panetta said he would not publicly discuss the secret surveillance missions that the drone incident has highlighted.
But he added that part of US efforts to defend both Afghanistan and the US homeland involve what he termed "important intelligence operations which we will continue to pursue".
Karzai, meanwhile, said Afghanistan doesn't want to be involved in any "adversarial relations" between the US and Iran.
The RQ-170 drone - known as the Sentinel - was lost over Iran two weeks ago. Iranian state television broadcast video of Iranians inspecting the aircraft, which was largely intact.