The car, which was believed to be carrying militants, was hit just outside the town of Bardere, which al Shabaab captured from government forces in 2009 and has controlled ever since.
Somali forces and the African Union-led peacekeeping force, known as AMISOM, have been advancing on the area over the past three days, officials say.
"Last night, a drone smashed an al Shabaab car believed to be carrying three officials," said local elder Nur Farah told Reuters on Thursday.
A spokesman from the militants could not immediately be reached for comment. An AMISOM spokesman also could not be reached.
Al Qaeda-linked al Shabaab, which wants to topple the Western-backed government and impose its strict interpretation of Islam on Somalia, has been driven out of major strongholds by the African and Somali forces but continues to launch bomb and gun attacks against officials, politicians and others.
