The Malian government in January called for military support from former colonial power France to help fight al-Qaida and foreign rebel groups tied to nomadic Tuaregs. Control over northern Mali was lost to militants following a 2012 coup.
Human Rights Watch said last week that two Tuaregs, who were arrested in February, died due to abuses by Malian forces and substandard detention conditions.
President of the National Commission for Human Rights Kadidia Sangare Coulibaly told the United Nations' humanitarian news agency IRIN that minority groups were among those who disappeared or were otherwise targeted following the French intervention.
"It is likely that some of these people, of whom we still have no news, were arrested on suspicion of supporting the Islamists," she said.
Malian state prosecutor Mohamed Dicko said hundreds of people were arrested in Gao and Bamako for allegedly supporting rebel groups.
European lawmakers last month said the French intervention "rescued Mali" but stressed more work was needed to put the country on the path toward stability.