The broadcasters were told to stop operating and report to the national security office on Tuesday.
"You should shut down upon receipt of this letter and appear at 10 am on Tuesday at the office of national security," said the letter, signed by Colonel Ahmed Hassan Ali and seen by Reuters.
The Somali government, which seized Mogadishu from an Islamist militia less than a month ago, is struggling to impose order on the city.
Since re-capturing Mogadishu with help from Ethiopia's military, its forces have come under sporadic attack from its enemies, most recently on Sunday.
Mixed response
Managers at HornAfrik and Shabelle, among the country's biggest independent broadcasters, both confirmed they shut down as ordered.
Al Jazeera said it had not been informed but saw no reason for such a move.
IQK could not immediately be reached for comment.
"Now that there is a government in place, they need to get a licence and avoid causing unrest by airing unconfirmed reports," Abdirahman Dinari, a government spokesman, said.
Dinari declined to say whether the move was carried out under sweeping emergency powers the parliament voted to give Abdullahi Yusuf, the president, on Saturday.
"If this is what state of emergency is meant, then it completely undermines the democratic values that the [interim government] has been proclaiming," the National Union of Somali Journalists said in a statement.
Troops offer
Also on Monday, Thabo Mbeki, the South African president, said South Africa would consider sending troops to Somalia but military operations elsewhere may limit its ability to deploy soldiers.
"Yesterday again I met the foreign minister of Kenya who had been sent by the East Africa region ... They are requesting we should assist with the deployment of troops in Somalia," he said in an interview on South African state television.
"I did say to the minister we will look at the matter this week."
Ethiopia, the main backer of Somalia's interim government, wants to withdraw its soldiers in the coming weeks.
Diplomats and aid agencies fear that their sudden withdrawal would leave a security vacuum around weak Somali government.