The single bench of Justice Sushila Karki has asked the government to refrain from implementing sections 3, 13, 23, 25 and 29 of the Ordinance. These sections are related with the formation of the commission, mandate of the commission, amnesty power and procedures of the commission and statute of limitation of the commission. The court found that these sections were in contradiction with the Interim constitution of Nepal and could not be implemented without amendments.

Advocates Madhav Basnet and Bishnu Pokhrel and representatives of victims' organizations Ram Kumar Bhandari and Suman Adhikary had filed separate petitions at the SC asking the court to nullify certain problematic provisions in the Ordinance that directly violate the rights of the victim. These provisions give powers to the Commission to grant amnesty to perpetrators without the consent of the victims and they are not clear about prosecuting the alleged perpetrators, the petitioners argued.

National Human Rights Commission has already expressed its discontent on the provisions of the TRC Ordinance by saying that they ignore victims' rights and let the perpetrators go scot-free. All amnesty provisions should be scrapped, NHRC maintained.

National and international human rights organizations too have taken strong exception against the content and process of TRC Ordinance. OHCHR chief Navi Pillay on 20 March issued a statement saying that the passing of the TRC Ordinance with amnesty provisions is regrettable. Accountability Watch Committee, a loose network of national human rights organizations in Nepal, announced that it will boycott the Commission as it was made as a part of the "opaque political deal" aiming at granting general amnesty even to those involved in cases of serious human rights violations.