"The troops came in, took our equipment and arrested our boss without explanation. We do not know why they are targeting us," Mohamed Abdullahi, a Shabelle radio staff member, told The Associated Press. Shabelle's director, Muqtar Mohamed Hirabe, was arrested.
A presenter and producer at Radio Horn Afrik, Mohamed Abukar, said troops broke down their doors and then ordered the station off air. The other shuttered station was Simba.
Government officials declined to comment on the raids.
The three stations and several other independent outlets were briefly taken off air three times last year, prompting criticism from press freedom watchdogs. At least eight journalists - including the owner and a presenter of Horn Afrik - were killed in separate attacks by unidentified gunmen in 2007.
The media have criticized both the government and the Islamic militants who have been trying to topple the administration through a bloody insurgency.
Somalia has been mired in chaos since 1991, when warlords overthrew dictator Mohamed Siad Barre.