The fragile Horn of Africa nation, which has battled an Islamist insurgency for over 16 years, has a history of defence cooperation with Turkey, hosting its largest overseas military base and training facility.
The alleged strikes on March 18 hit a farm near Bagdad village in the southern Lower Shabelle region, killing nearly two dozen people and injuring 17 others, mostly children, the rights group said.
Residents told Amnesty "the drone strikes followed heavy ground fighting" between Al-Shabaab jihadists and Somali security forces, the watchdog said.
Investigators interviewed 12 people, including victims, their relatives and witnesses, and analysed satellite imagery and photos of weapon fragments to establish the use of Turkish-manufactured bombs and TB-2 drones.
Mohamed Ali Deerey, who lost his younger brother and nine-year-old nephew in the attack, told Amnesty he hurried to the farm as soon as he heard the first blast, just before the second strike claimed the lives of more people.
"The scene was chaotic. There were screams, blood, and bodies all over the ground," he said.
Another person, who lost six members of their family, said they were "horrified".
"This is inhumane. This is a massacre."
Amnesty said all five families affected by the strikes belonged to "the marginalised Gorgaarte clan".
"In Somalia, civilians have borne the brunt of suffering in war far too often. These horrific deaths must not be overlooked," said Tigere Chagutah, Amnesty's regional director for east and southern Africa.
"The Somali and Turkish governments must investigate these deadly strikes as a war crime, and put an end to reckless attacks on civilians."
- Defence deal -
Somalia's government said it had conducted an operation targeting Al-Shabaab in the same area, but did not mention any civilian deaths.
"More than 30 (militants) were killed during an operation jointly carried out by the Somali national armed forces and international partners", the ministry of information said in a statement on March 19.
It said 24 jihadists "were killed in the operation in the Baldooska area while 15 others had been killed in an airstrike on Bagdad."
Amnesty said it had requested further details from the Somali and Turkish governments but had not received any response.
The two governments signed a maritime defence deal in February this year.
Turkey is among several nations training Somali soldiers to take over from an African Union peacekeeping mission, whose troops are set to leave by the end of the year.
Although Al-Shabaab was forced out of Mogadishu by an AU force in 2011, the jihadists retain a strong presence in rural Somalia and have carried out numerous attacks against political, security and civilian targets.
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