Amnesty International has accused the Malian army of committing serious human rights abuses, and violations of international humanitarian law, including executing civilians.
The evidence was uncovered during a ten-day research trip to the country.
Amnesty says Islamist armed groups have committed serious human rights violations, including unlawful killing and the recruitment of child soldiers.
The organisation also says there is evidence of that civilians, including children, were killed in an airstrike carried out by French-led forces.
Researcher Gaëtan Mootoo said:
Many people are genuinely afraid of being arrested, or worse, by the military. The security forces must ensure that people are protected from any reprisals based on ethnicity or perceived political sympathy.
The authorities should also immediately launch an independent and impartial investigation into any reports of extrajudicial executions by the armed forces, and suspend any security personnel suspected of involvement in human rights violations.
Throughout ten months of Islamist rule, the people of Timbuktu risked their lives to preserve the artefacts of their ancient heritage.
Francois Hollande is due to visit Timbuktu during his visit to the West African country this weekend. He will be welcomed by many.
Downing Street have been explaining what offers the UK have made to the military effort in Mali.