The strike on Adan Yabaal, 220 kilometres (140 miles) north of the capital Mogadishu came as Al-Shabaab fighters raided the key town used as a base by Somali military commanders.
Growing attacks by the Al-Qaeda-linked group, including one on President Hassan Sheikh Mohamud's convoy, are fuelling worries of a jihadist resurgence after militants were forced back in recent years.
The strike on Wednesday night by Somali armed forces and the US Africa Command "aimed to neutralize the threat posed" by Al Shabaab, the information ministry said in a statement posted on X.
"The targeted strike hit a site used by the militants as a gathering and hideout," it said. "Preliminary reports indicate that 12...operatives, including senior leaders, were eliminated."
Somali government forces took control of Adan Yabaal from Al-Shabaab in December 2022 during the major offensive backed by African Union peacekeeping forces.
On Wednesday, Al-Shabaab launched a dawn raid on the town, with bombs loaded on trucks detonating before militants fought their way into the town, a military official said.
The official said the army was getting reinforcements from nearby positions to defend the town, but Al-Shabaab claimed its fighters had overrun the Somalia military and controlled Adan Yabaal.
AFP was unable to confirm those claims.
Two local residents told AFP that militants had taken Adan Yabaal.
The president had visited the town recently, with state media reporting he had met with military commanders to review the ongoing military offensive against Al-Shabaab.
In the southwest, Somali forces and allies killed 35 militants around Baidoa town in the early hours of Thursday, after they attempted to attack an army base there, the ministry said.
Earlier this month, Al-Shabaab fired multiple mortar rounds near Mogadishu's airport, disrupting international flights.
Halane camp -- a fortified compound that houses the United Nations, aid agencies, foreign missions and the headquarters of the African Union's Support and Stabilisation Mission in Somalia (AUSSOM) -- was also targeted.
The group has seized key locations in Middle and Lower Shabelle, coastal regions on either side of Mogadishu.
A bomb blast that narrowly missed the convoy of President Mohamud in March underscored that Al-Shabaab again poses a risk in the capital itself.
Al-Shabaab has been fighting the government for 15 years, but the African Union-led peacekeeping force helped push the jihadists onto the defensive in 2022 and 2023.
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