A statement Monday said it is thought that Ali Mohamed Hussein died in the operation near Tortoroow, an al-Shabaab stronghold in the Lower Shabelle region of southern Somalia.
Ali had served as the extremist group's shadow governor for Mogadishu and had been one of its most outspoken officials.
Somalia's statement comes hours after the U.S. military said a drone strike killed an al-Shabaab member on Saturday near Tortoroow.
A statement from the U.S. Africa Command said the airstrike occurred Saturday and that no civilians were killed.
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U.S. President Donald Trump earlier this year approved expanded military operations against al-Shabaab, including more aggressive airstrikes and considering parts of southern Somalia areas of active hostilities.
The al-Qaeda-linked al-Shabaab is the deadliest Islamic extremist group in Africa.
* Al-Shabaab senior official killed in Somalia airstrike, U.S. says
The U.S. statement said the airstrike was carried out in co-ordination with regional partners "as a direct response to al-Shabaab actions, including recent attacks on Somali forces."
The Somali intelligence official identified the targeted al-Shabaab leader as Hussein, who had served as the extremist group's shadow governor for Mogadishu and had been one of the group's most outspoken officials.
MISSILE STRUCK CAR
The official said at least one missile struck a car that the al-Shabaab leader had been travelling in near Tortoroow. One person was killed, said the official, who spoke on condition of anonymity because they were not authorized to speak to the press.
In early July, the U.S. military said it carried out an airstrike against al-Shabaab in Somalia and was assessing the results. The airstrike followed one in June that the U.S. said killed eight extremists at a rebel command and logistics camp in the south.
The Somalia-based al-Shabaab earlier this month mocked U.S. President Donald Trump for the first time, in a video that called him a "brainless billionaire."
The extremist group also has vowed to step up attacks in Somalia after the president elected in February declared a new offensive against al-Shabaab, which continues to carry out deadly attacks in the capital of Mogadishu.
The extremist group also has carried out deadly attacks in neighbouring countries, notably Kenya, calling it retribution for sending troops to Somalia to fight al-Shabaab.