One man told the London-based rights group he had lost his wife and six of his children in the night-time air raid on the area of Amasrakad on March 17.
The army had described the two strikes as "having contributed to neutralizing many terrorists," Amnesty said, but that claim was refuted by the accounts of seven survivors and witnesses.
A first strike hit a pick-up truck, then a second struck a makeshift shelter where residents had sought refuge, killing nine people instantly, Amnesty said.
Three more people died of their wounds and a woman discovered later that her unborn fetus had died.
"It is unconscionable that whole families could be killed by drone strikes, without any accountability or justice," said Amnesty's Samira Daoud.
"Authorities in Mali must ensure an effective and independent investigation into the killings of these civilians."
Mali has since 2012 been ravaged by different jihadist groups affiliated to Al-Qaeda and the Islamic State group, as well as by self-declared self-defence forces and bandits.
The country has been under military rule since back-to-back coups in 2020 and 2021, with the security situation compounded by a profound humanitarian and political crisis.
Amnesty says the army has intensified military operations against Al-Qaeda, IS and former rebel groups since mid-2023, regularly conducting drone strikes.
It said an increase in military operations in the regions of Kidal and Gao over the last few months had pushed many people to flee to Amasrakad.
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