The self-styled Libyan National Army, commanded by strongman Khalifa Haftar, controls much of eastern Libya and is battling an array of jihadist groups who seized Benghazi in 2014.
The LNA announced on Saturday that "terrorist groups" had fled their last stronghold in Benghazi and that its forces were in full control of the city.
Human Rights Watch said the LNA "may have committed war crimes, including killing and beating civilians and summarily executing and desecrating bodies of opposition fighters," in the eastern city over the weekend.
"The LNA leadership needs to respond urgently to these deeply disturbing allegations by investigating the suspected perpetrators, including senior military commanders who may bear individual responsibility," said Joe Stork, deputy Middle East director of the New York-based group.
The United Nations' Libya envoy Martin Kobler tweeted today that he was "appalled" by the reports.
"Impunity must end. Call for credible investigations & holding perpetrators accountable," he tweeted, adding that those responsible could be liable for trial at the International Criminal Court.
Persistent chaos in Libya since the 2011 ouster and killing of dictator Moamer Kadhafi has seen a range of armed groups battle for control of the country.
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