On Monday, authorities in the turbulent Horn of Africa nation shut down Shabelle Radio and briefly detained two of its senior staff. It and other independent local broadcasters have been accused by the government of supporting the rebels.
"They said the order to close the radio station will affect all independent stations in Mogadishu," Mustafa Haji, chief editor of Simba Radio, told Reuters.
At Radio Banadir, the other station shut down on Tuesday, workers fled when heavily-armed troops entered the compound.
"They terrorised the employees... All the reporters panicked and ran," said its deputy director, Ali Muhamed Aden.
With rampant insecurity largely keeping foreign correspondents out of Somalia, local journalists have been left to report on the insurgency targeting the interim government and its Ethiopian military allies.
The latest round of fighting with the rebels has killed at least 70 people and driven tens of thousands from their homes.
Reporters Without Borders, a Paris-based watchdog, said the Somali authorities were showing contempt towards the free media.
A journalists' group in Somalia said the government's actions were "absolutely intolerable".
Shabelle, which remained off the air on Tuesday, said on its Web site that it had received no explanation for its closure or been told how long it would last. It said it was the eighth time this year that the government had shut it down.
"There has been pressure, intimidation and death threats to the journalists from the government and other people," it said.
Eight local reporters have been killed in the line of duty in Somalia this year, most of them shot down by unknown gunmen.
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