The stations, HornAfrik radio and television, Shabelle Media Network and Radio Voice of Holy Koran, were shut down on 6 June, for alleged support of anti-government elements.
"We condemn the closure of these three radio stations," said Joel Simon, executive director of the Committee to Protect Journalists. "The authorities have silenced independent voices on the basis of unsubstantiated accusations. We call on the Somali transitional government to allow these broadcasters back on the air immediately."
HornAfrik managing partner, Ali Iman Sharmarke, said his station was shut down after a visit at 1pm (11am GMT) by senior government officials accompanied by armed men. The visitors presented a letter signed by the minister of information, Madobe Nuunow Mohamed, ordering the station to shut down and cease operations.
"We have been off the air ever since, and we don't know how long we will remain so," he said.
Mohamed Amin Sheikh Adow, the deputy chairman of the Shabelle Media Network, told IRIN he received a similar letter at the same time.
The two media houses are the biggest in the Somali capital of Mogadishu and have the largest audiences.
According to Sharmarke, the media groups were accused of supporting "extremist and terror groups".
He added: "The bottom line is they [the government] accused us of being anti-government."
A government spokesman, Abdi Haji Gobdon, confirmed the closures, saying the media groups were shut down on orders of the National Security Council. He accused the media houses of engaging in activities detrimental to national security and of "carrying programmes supporting extremist elements".
Sharmarke denied the accusations, saying the closures were "the usual harassment of the free media and a denial of free expression of the Somali people".
Journalists' groups and civil society in Mogadishu condemned the action, while Sheikh Adow of Shabelle radio said the accusations against the media were baseless. "We have always maintained international media standards."
Blow to talks
Meanwhile, a prominent Hawiye elder, Haji Abdi Iman, the chairman of the Hawiye Council of Elders, was arrested on 6 June by the government and is still in custody, according to Ugas Abdi Dahir Ugas Nur, a member of the council.
Civil society members in Mogadishu condemned the arrest and said it was a setback for the reconciliation process. There has been hope that the ongoing talks between the Hawiye clan elders and the government would lead to an improvement in the security situation in capital, which would in turn lead to a return of the displaced, said the source.
Fighting in the city, which started in February between Ethiopian-backed Somali government troops and insurgents comprised of the remnants of the Islamic courts and Hawiye militia, claimed more than 1,000 lives and displaced another 400,000 people.