The unidentified suspects were travelling in a vehicle in the town of Qoton in Hadramawt province when they were targeted, the sources said.
The United States is the only country known to operate armed drones over Yemen, home to what it considers to be Al-Qaeda’s most dangerous affiliate.
It has kept up strikes on jihadists during months of fighting between pro-government forces and Iran-backed Huthi rebels who control the capital.
Al-Qaeda has exploited the turmoil to tighten its grip on parts of southeast Yemen, seizing Mukalla, capital of Hadramawt province, in April.
The Saudi-led coalition that has been supporting pro-government forces fighting the Huthis and their allies has not targeted the jihadists so far.
But Yemeni Prime Minister Khaled Bahah said on Tuesday that confronting the extremists was inevitable in the future.