In July 1966, the position of Deputy Army Commander was created and Panggabean was appointed to the position to assist Suharto with his increasing workload. In 1967, Panggabean became Army Commander himself. As Army Commander, Panggabean witnessed a reorganization in the Indonesian National Armed Forces which saw the armed services commanders be reduced in status to chief of staffs under the control of an Army commander, a position to be filled by Suharto himself. In 1969, Panggabean became the Commander of Kopkamtib. Two years later, in 1971, Suharto reshuffled the Cabinet and Panggabean became Deputy Commander in addition to becoming State Minister assisting the President in matters of Defense and Security.