Main article: Operation Searchlight
Location of Bengali and Pakistani military units during Operation Searchlight, March 1971
A planned military pacification carried out by the Pakistan Army – codenamed Operation Searchlight – started on 25 March to curb the Bengali nationalist movement by taking control of the major cities on 26 March, and then eliminating all opposition, political or military, within one month. Before the beginning of the operation, all foreign journalists were systematically deported from East Pakistan.
The main phase of Operation Searchlight ended with the fall of the last major town in Bengali hands in mid-May. The operation also began the 1971 Bangladesh atrocities. These systematic killings served only to enrage the Bengalis, which ultimately resulted in the secession of East Pakistan later in the same year. The international media and reference books in English have published casualty figures which vary greatly, from 5,000–35,000 in Dacca, and 200,000–3,000,000 for Bangladesh as a whole, and the atrocities have been referred to as acts of genocide.
According to the Asia Times,
At a meeting of the military top brass, Yahya Khan declared: "Kill 3 million of them and the rest will eat out of our hands." Accordingly, on the night of 25 March, the Pakistani Army launched Operation Searchlight to "crush" Bengali resistance in which Bengali members of military services were disarmed and killed, students and the intelligentsia systematically liquidated and able-bodied Bengali males just picked up and gunned down.
Although the violence focused on the provincial capital, Dacca, it also affected all parts of East Pakistan. Residential halls of the University of Dacca were particularly targeted. The only Hindu residential hall – Jagannath Hall – was destroyed by the Pakistani armed forces, and an estimated 600 to 700 of its residents were murdered. The Pakistani army denied any cold blooded killings at the university, though the Hamood-ur-Rehman commission in Pakistan concluded that overwhelming force was used at the university. This fact, and the massacre at Jagannath Hall and nearby student dormitories of Dacca University, are corroborated by a videotape secretly filmed by Professor Nurullah of the East Pakistan Engineering University, whose residence was directly opposite the student dormitories.
The scale of the atrocities was first made clear in the West when Anthony Mascarenhas, a Pakistani journalist who had been sent to the province by the military authorities to write a story favourable to Pakistan's actions, instead fled to the United Kingdom and, on 13 June 1971, published an article in the Sunday Times describing the systematic killings by the military. The BBC wrote: "There is little doubt that Mascarenhas' reportage played its part in ending the war. It helped turn world opinion against Pakistan and encouraged India to play a decisive role", with Indian Prime Minister Indira Gandhi herself stating that Mascarenhas' article has led her "to prepare the ground for India's armed intervention".
Hindu areas suffered particularly heavy blows. By midnight, Dacca was burning, especially the Hindu-dominated eastern part of the city. Time magazine reported on 2 August 1971, "The Hindus, who account for three-fourths of the refugees and a majority of the dead, have borne the brunt of the Pakistani military hatred."
Sheikh Mujibur Rahman was arrested by the Pakistani Army. Yahya Khan appointed Brigadier (later General) Rahimuddin Khan to preside over a special tribunal prosecuting Rahman with multiple charges. The tribunal's sentence was never made public, but Yahya caused the verdict to be held in abeyance in any case. Other Awami League leaders were arrested as well, while a few fled Dacca to avoid arrest. The Awami League was banned by General Yahya Khan.