The car was hit as it drove along a side road in Shabwa's Bihan district, the official, from forces loyal to President Abedrabbo Mansour Hadi's internationally recognised government told AFP.
The US military is the only force known to operate armed drones over Yemen.
The security official said the militants were members of al Qaeda, and said the aircraft that carried out the strike was American.
UN envoy holds 'fruitful' talks with Yemen rebel chief
The United States considers the Yemen-based al Qaeda in the Arabian Peninsula to be the radical group's most dangerous branch.
A long-running drone war against AQAP has intensified since US President Donald Trump took office in January 2017.
AQAP has flourished in the chaos of the country's civil war, which pits the Saudi-backed government against Huthi rebels.
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