Human Rights Watch said it has learned that police in the Himalayan kingdom are allegedly refusing to register First Information Reports (FIRs) filed on behalf of the victims.
"Despite endless promises of reform, impunity remains the norm in Nepal," Asia director at Human Rights Brad Adams said.
"Accountability for any abuses by both protesters and police are important, and unfortunately at the moment it looks as if alleged abuses by the police will simply be forgotten."
The rights group said security forces had often clashed with the protesters over months of violence, leading to deaths, abuses and injuries on both sides.
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In October 2015, Human Rights Watch documented the 25 killings, including of 9 police officers and 16 protesters or bystanders.
By the time the protests ended in early 2016, around 55 people had died.
"While arrests were made for violent attacks against the police, the government has not yet taken any steps to ensure that members of the security forces are held to account for serious human rights violations during the protests," the group said.
In its letter, Human Rights Watch made specific recommendations to the government of Nepal on necessary steps to ensure accountability for these violations including acting on the findings of the National Human Rights Commission to ensure appropriate disciplinary and legal action in cases of excessive use of force, arbitrary arrests and torture.