Rival ethnic militias have clashed over land and politics this year
An international lobby group has called for military aid to Kenya to be halted until an inquiry is held into a crackdown in the west of the country.
Human Rights Watch (HRW) says dozens of people have "disappeared" in Mount Elgon after local men were rounded up.
The operation was intended to tackle an ethnic militia, known as the Sabaot Land Defence Force (SLDF), accused of running an 18-month terror campaign.
HRW accuses both sides of committing war crimes in the area.
The security forces have denied repeated complaints of wrongdoing in the area and have blamed any human rights violations on the militia.
HRW says 37 people remain "disappeared", while local human rights groups say more than 70 people have been killed.
Witnesses told researchers that much of the male population had been rounded up.
"The 'successful' operation to tackle the rebellion in Mt Elgon has come at a terrible cost," said Georgette Gagnon, Africa director at Human Rights Watch.
"The government should urgently produce those who have disappeared and ensure that those responsible for torture and other crimes, including the commanders, are held accountable."
In May, the state-funded Kenya National Commission for Human Rights (KNCHR) said the defence minister and army chiefs should face prosecution over the alleged torture of civilians in Mt Elgon.
HRW accuses the SLDF of killing more than 600 people in the past two years.
The SLDF says it is fighting for ancestral land belonging to the Sabaot community.