Security forces in Mali, Niger and Burkina Faso have been accused of unlawfully killing or causing the disappearance of around 200 people.
Forces in Mali, Burkina Faso, and Niger have launched offensives against militants linked to al Qaeda and the Islamic State in the Sahel region, south of the Sahara desert.
Islamist militants first emerged in Mali in 2012, and then spread to Burkina Faso and Niger.
"The deliberate killings of unarmed civilians by security forces in Mali and Burkina Faso may constitute war crimes under international law and should be thoroughly investigated," said Amnesty.
Mali's defence minister vowed to investigate allegations, including charges that soldiers killed 43 people during attacks on two villages last week.