Sanogo led a March coup that toppled the civilian leadership in Bamako. Opposition forces attempted a counter-coup in April. Human Rights Watch said nearly two dozen fighters opposing Sanogo were forcibly disappeared.
Daniel Bekele, director of African affairs at Human Rights Watch, said in a statement from Kenya that the interim administration in Mali has a responsibility to hold those responsible for atrocities accountable.
"Even at this chaotic and difficult time in Mali, authorities should ensure that the horrific treatment and other violations should be promptly addressed," he said in a statement.
His group said it suspects the disappeared are dead.
The International Criminal Court announced last week that it started a preliminary investigation into possible crimes in Mali. The country's justice minister requested the investigation.
In the north of the country, Islamic rebels, including some aligned with al-Qaida, have razed protected heritage sites in Timbuktu, saying they weren't in line with their interpretations of Shariah law.