The weak central government claims the group is spreading propaganda from at least two radio stations, including Mogadishu's Holy Quran radio, a private FM station, which it took earlier this week.
Al-Shabaab earlier this year looted private radio equipment to use in a station, the government said.
"We strongly condemn these acts. They want to silence the independent media with brutality and intolerance," said Abdirahman Omar Osman, Somalia's minister of information.
Al-Shabaab, which has pledged allegiance to al Qaeda, controls much of southern Somalia and portions of Mogadishu. It follows the strict Saudi Arabian-inspired Wahabi interpretation of Islam, rather than the Sufi Islam of many Somalis.
In a statement issued earlier this week, al-Shabaab said all radio equipment belonged to Somali Muslims and that listeners in the capital will enjoy religious programs and other coverage.
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