In 1971, when the talks with Awami League failed, Ali along with Lieutenant-General Tikka Khan launched the military crackdown on the people of erstwhile East Pakistan under direction of President Yahya Khan. Ali is held responsible for widespread genocide and massacre took place in Dhaka University. Hamoodur Rahman Commission though heavily criticized other senior military staff of Pakistan Army in East Pakistan at the time including confirmation of mass atrocities, cleared Ali citing the fact that he was not involved in any direct Military Operation due to the nature of his post which was mostly Administrative.