Served as Britain's secretary on the Combined Policy Committee, gaining access to classified information about British and American plans regarding atomic energy and nuclear weaponry. He was also given access to information from the United States Atomic Energy Commission. Worked alongside Alger Hiss, a U.S. State Department official regarding plans for the United Nations. Discussed U.S. policy on a number of topics, including U.S. Military participation in South Korea.

Continued his trips to New York, unaware that passages in the Venona documents described a Soviet spy who also visited New York at the same time (in July 1946).

The documents were transmitted accidentally with a lower security encryption and included information from transmissions between British Prime Minister Winston Churchill and U.S. President Harry Truman, including specific serial numbers for those transmission. The serial numbers helped to narrow down the number of people who would have had access to the documents. This information, in addition to his constant requests to participate in meetings of the Atomic Energy Commission led the CIA to maintain surveillance of him.

James Angleton, head of the CIA's counter-intelligence program, determined that Maclean was indeed a Soviet spy and caused his pass to the Atomic Energy Commission to be revoked. Angleton informed MI5 of his suspicions and Kim Philby was apprised of the situation. Philby warned Soviet officials and they informed Maclean of the situation.

Maclean, a known bi-sexual, was observed in drunken stupors, prowling for homosexual liaisons. His drinking grew to a dangerous level until he was recalled by the British government and returned home in 1948. He was transferred to Cairo, Egypt where he served as chancery for the British Embassy but again suffered from drunken episodes and was again recalled to London in 1950. Nonetheless, in early 1951 he was assigned a new position, this time as head of the American Department of the Foreign Office.