Both sides in Nepal's 1996-2006 civil war between Maoist guerrillas and the state were accused of serious human rights violations including rape, but no one has yet been prosecuted.
The report is based on the testimonies of more than 50 women -some of whom were just schoolgirls when they were attacked. It calls for the government to revise its 35-day time limit and to provide reparations to victims.
"For more than 10 years already, these women have suffered in silence and fear while the perpetrators have walked free," said Meenakshi Ganguly, South Asia director at Human Rights Watch.
"Justice and reparations for women who suffered sexual assault is long overdue unfinished business from the civil war."
Nepal is in the process of setting up two commissions to investigate wartime crimes and heal wounds from the conflict.
Although lawmakers have barred the commissions from offering amnesty in cases of sexual violence, HRW warned that unless the statute of limitations is overturned, enabling investigations of wartime rapes, victims will not have access to justice.
Some of the women interviewed described how soldiers targeted female relatives of suspected Maoists, while others spoke of rapes by rebels who forcibly recruited women into the insurgency.
A victim identified by the pseudonym, Shona, said she was accused of being a Maoist and raped repeatedly by a police official who would come to her house while her husband worked overseas.
"He used to kick (the door) and come inside. I was alone. The children used to run away as soon as the police came... he used to rape me", she said.
Shona said she and her husband tried to register a criminal case after the war ended, but were told that "nothing can be done".
The Supreme Court in 2008 ordered a revision of the 35-day limit for reporting rapes, calling it an "unreasonable" and "unrealistic" provision, but the law still stands.
Unlike the families of those who were killed or targeted in "forced disappearances" during the war, rape victims have not been included in the government's interim compensation programme and have received no financial support, HRW said.
"If the government is serious about addressing conflict-era sexual violence and its fallout, it needs to include survivors of sexual violence as part of its compensation package," Ganguly said.
"The complete silence on providing interim relief, combined with the rampant culture of impunity, drives these victims further into invisibility."
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