Former Maoist rebels and security forces have been accused of carrying out torture, killings, rapes and "forced disappearances" during the conflict, which ended in 2006 leaving more than 16,000 dead.
The ruling Communist Party (Unified Marxist Leninist) of Nepal and its coalition partner, the Maoists, last week signed an agreement paving the way for war crimes cases to be withdrawn or pardoned.
In a joint statement, Amnesty International, Human Rights Watch and the International Commission of Jurists (ICJ) accused the two parties of attempting to "wash away the crimes of the conflict" with the new agreement.
Nepal's Supreme Court has repeatedly opposed attempts to grant amnesty for serious rights abuses.
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The Himalayan nation set up two post-war commissions for transitional justice in 2015, which began to accept complaints from victims last month.
The Truth and Reconciliation Commission and Commission for Enforced Disappearances were agreed as part of the peace pact signed between the Maoists and the government in 2006.
An army colonel, who was arrested in January 2013 in Britain over allegations of torture committed during the war, is also facing trial in a British court.