The dawn attack also badly damaged the offices of public water and telecommunications utilities in Huta, capital of Lahij province, the official added.
No details about the three victims were immediately available.
Witnesses said two drones overflew Huta both before and after the attack.
The drone strike came a day after a soldier and a civilian were killed in a suicide car bombing in Huta that a Yemeni military source said targeted an armoured vehicle of the Emirati armed forces.
Lahij is one of five provinces retaken from Iran-backed Shiite Huthi rebels last summer by pro-government forces, but security problems persist.
Since the coalition intervened in Yemen, Sunni jihadists of Al-Qaeda and also the Islamic State group have exploited the chaos created by the conflict to strengthen their positions in the south.
Al-Qaeda has been well-established for years in south Yemen, but now faces competition from IS which has mounted a series of deadly attacks, particularly in Aden, temporary capital of the internationally recognised government.
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