In late December 1963, a relic believed to be a hair of the Islamic prophet Muhammad reportedly went missing from the Hazratbal Shrine in Srinagar, Kashmir, prompting mass protests in Jammu and Kashmir. Pakistani President Muhammad Ayub Khan, speaking at Dhaka airport, stated he would not be responsible for any reaction in Pakistan to the incident. Although the relic was recovered on 4 January 1964, tensions had already escalated, and Pakistan Radio subsequently described the recovered relic as fake, further inflaming sentiment.
Violence against Bengali Hindus began in Khulna on 2 January 1964, where Hindus were barred from wearing shoes, using umbrellas, or riding rickshaws as a mark of mourning for the relic. Processions calling for violence against Hindus were followed by attacks beginning around 4 p.m., with mobs — reportedly numbering in the thousands and including workers from local industries — looting, burning, and killing over the following days. Sources describe several hundred Hindus killed at Khulna Launch Ghat and further deaths at Mongla port. Abdus Sabur Khan, then Communications Minister of Pakistan, is described as having addressed crowds with anti-Hindu rhetoric during this period; he has not been reported as charged with any offense in relation to these events.
In Dhaka, violence intensified from 13–18 January 1964. Hindu passengers were removed from trains; homes, temples, a hospital, a library, and a hostel were destroyed; and killings were reported at multiple locations, including the Ramakrishna Mission at Tikatuli and the Rayerbazar area, where the source states 96 Bengali Hindus were killed and the locality was subsequently renamed. A 24-hour curfew was imposed on 18 January. Press reports cited by the source estimated thousands homeless and up to 1,000 killed in Dhaka within a week, with one nurse's account citing 600 dead at a single hospital.
In Narayanganj, mill workers reportedly attacked Hindu residential areas beginning 13 January, with more than 700 people said to have been killed near the Dhakeshwari Cotton Mills, and tens of thousands sheltering at the Lakshminarayan Cotton Mills compound without food for days. Additional killings were reported in surrounding villages, and an academic, described as a professor, was reportedly stabbed to death while photographing the violence. The source states approximately 3,500 Hindus were killed and 80,000 rendered homeless across the Narayanganj sub-division. Violence and land seizures were also reported in Rajshahi, Sylhet, and Mymensingh, the latter particularly affecting Garo and Hajong communities.
The East Pakistan government imposed an ordinance restricting property sales by Hindus and enforced press censorship. The violence produced a large refugee exodus to India, with an estimated 135,000 Bengali Hindu refugees arriving in West Bengal and roughly 75,000–78,000 tribal refugees, including many Christians, fleeing to Assam. Refugees were sheltered in relief camps in Dhaka, Assam, West Bengal, and Tripura, with resettlement later occurring in the Dandakaranya region of India.