The agency also noted that Iran had not allowed it access to another suspected site where there was evidence of past nuclear activity.
Trump asked his top national security aides what options were available and how to respond, officials said.
After Pompeo and Milley described the potential risks of military escalation, officials left the meeting believing a missile attack inside Iran was off the table, according to administration officials with knowledge of the meeting.
Trump might still be looking at ways to strike Iranian assets and allies, including militias in Iraq, officials said. A smaller group of national security aides had met late Wednesday to discuss Iran, the day before the meeting with the president.
White House officials did not respond to requests for comment.
Since Trump dismissed Defence Secretary Mark T. Esper and other top Pentagon aides last week, Defence Department and other national security officials have privately expressed worries that the president might initiate operations, whether overt or secret, against Iran or other adversaries at the end of his term.
New York Times