After attending the Armed Forces War College and graduated with MSc in Strategic studies in 1971, Lt.Col. Beg was stationed in East-Pakistan to serve as a military adviser to the Eastern Command led by its GOC-in-C, Lieutenant-General A.A.K. Niazi. Upon arriving and observing the military deployments and actions, Lt.Col. Beg became very critical of Gen. Niazi's strategy and eventually became involved in acrimonious argument with his Gen. Niazi's staff in Dacca, having been very critical of armed forces interference in the political events in East. His open mindedness and arguments with his senior officer eventually led his transfer back to Pakistan and was threatened with facing the court martial.