The raid targeted their vehicle on Tuesday evening near the border of Baida and Shabwa provinces, the official said.
The United States is the only country known to operate armed drones over Yemen.
’US drone’ kills three Qaeda suspects in Yemen: tribal sources
It has kept up strikes on militants during months of fighting between pro-government forces and Shia Houthi rebels who control the capital.
Yemen, home to what the United States considers al Qaeda's most dangerous affiliate, has been convulsed by unrest since the Iran-backed Houthis seized Sanaa in September last year.
Al Qaeda in the Arabian Peninsula (AQAP) has exploited the turmoil to tighten its grip on parts of southeast Yemen, including Mukalla, the capital of Hadramawt province, imposing a strict form of Islamic law.
Four al Qaeda suspects killed by 'US drone' in Yemen: official
Militants, including AQAP and the Islamic State group, have also gained ground in and around the main southern city of Aden, where a Yemeni naval officer was shot dead overnight by unknown gunmen, security officials said.
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