During the operation, there were numerous instances of army atrocities, including rape, torture, and killing of civilians, which was unearthed by several human rights organizations.

[9] Enjoying a soft-eye of the AGP government (1985–1990), the organization became strong with a large recruitment drive and the killing of many Congress leaders, police officers, and civilians.

The Asom Gana Parishad led state government was held responsible for the poor law and order situation.

[16] The then BJP president and MP L K Advani demanded the dismissal of the Assam government and sought Army action against the ULFA in parliament debate.

[17][18] The Prime Minister Chandra Shekhar had to take the decision to dismiss the Assam government and order Army action against the ULFA.

[51][52] On 8 January 1991, the then Governor of Assam Devi Das Thakur announced that the Indian government is open for a lateral talk with the ULFA.

Prime Minister Chandra Shekhar too announced the same in Rajya Sabha, and, in February 1991, the ULFA declared a unilateral ceasefire.

[57] Human Rights organization Amnesty International asserted that, during operation Bajrang, villagers of Assam were terrorized as the Indian army committed violence of rape, murder, and illegal arrests.

[59][60][61] There were also parliamentary debates in the Rajya Sabha of India about the rapes committed by the Indian Army during Operation Bajrang.

[55] During the operation, most of the senior leaders escaped to their Bangladesh's camp in Sherpur, but Sunil Nath and Paresh Baruah stayed in Assam to continue the militancy activities.

[72][73] In 2013, KPS Gill, who served as the Director general of police of Assam and Punjab, opined that Operation Bajrang was not necessary as it created mistrust between Security forces and civil society and also took lives of many innocent people.