Radio Shabelle and its sister station Sky FM were shut down Friday and 21 people arrested, after they were reportedly critical of a military operation to disarm a militia leader in the capital Mogadishu that escalated into heavy gun battles.
"Both radio stations were encouraging the public to take up arms against government forces," the information ministry said in a statement.
"As a result of these broadcasts there were demonstrations in some parts of the city that led to the killing of innocent people."
Eighteen workers, including journalists, technicians and guards, were released within two days, but a court has ordered three senior staff be held pending an investigation.
"Three people remain in custody as we believe that they were responsible for the provocative broadcasts," Attorney General Ahmed Ali Dahir said in the statement.
Dahir said a court order had been issued to hold them for 21 days.
"After we complete our investigation we will bring them to court to face trial," he said.
The three are radio station owner Abdimalik Yusuf Mohamud, Sky FM director Mohamud Mohamed Dahir, and Shabelle deputy news editor Ahmed Abdi Hassan.
Reporters Without Borders (RSF) alleged the three had been beaten in custody.
"Several witnesses, including security officers, say the three men have been badly tortured in an attempt to extract confessions," RSF said.
But Dahir said investigations had "found no substance to the allegations."
The stations resumed broadcasting on Tuesday.
Radio Shabelle has been briefly shut by the government at least three times in recent years.
It has also been threatened by Somalia's hardline Shebab fighters over its reporting, and several of its journalists and two of its directors have been killed.