Mali in January called for military support from former colonial power France to help stop al-Qaida and foreign militants. Control over northern Mali was lost to militants in an early 2012 coup.
Deputy High Commissioner for Human Rights Kang Kyung-wha told the Human Rights Council there was a general sense that Tuareg and other ethnic communities might be targeted by Malian forces for their perceived support of militant forces.
"Those who remain in the country are afraid of being targeted not for what they have done, but for who they are," she said.
Field reports from the Office of the High Commissioner for Human Rights said incidents of reprisal attacks escalated following the French intervention.
"We call on the Malian authorities to protect the communities at risk and to ensure that their troops act in accordance with human rights law and international humanitarian law," Kang said.
The International Committee of the Red Cross last week said that despite Malian and French progress, Mali isn't secure.