The group urged the Republic of Congo to investigate the crimes and bring the soldiers to justice.
The February exhumation of a grave near a peacekeeping base uncovered the remains of 12 people who peacekeepers said had escaped after being detained in March 2014, the rights group said. It also documented death by torture of two Christian militia leaders in Bossangoa in December 2013, a public execution of two suspected militia members in February 2014 and the deadly beating of two civilians in June 2015 in Mambere.
Human Rights Watch said it wrote to Republic of Congo President Denis Sassou N'Guesso urging investigations.
Troop-contributing countries to AU and U.N. Peacekeeping missions are responsible for holding their forces accountable.
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The new report says a Christian militia leader clashed with peacekeepers in 2014, killing one, and peacekeepers later surrounded the leader's home, detaining about 12 people. Five women, including one who was pregnant, and two children aged seven months old and 10 were among those detained.
The AU temporarily suspended the commanding officers in Boali and Bossangoa in June 2014, and their soldiers were redeployed elsewhere in the country, the report says.
A U.N. Peacekeeping mission took over from the African Union force in September 2014 and insisted the Republic of Congo peacekeepers be replaced.