One channel is controlled by a prominent Sunni Arab politician and the other is based in Saddam's Sunni home region.
"Let them reject the verdict, they have the right, but don't talk about 'mujahideen' and 'resistance'," said Abdul Karim Khalaf, an interior ministry spokesman, accusing the stations of giving a platform to people who were making threats of violence.
"They are hosting people who are talking about something that is completely distinct from politics, calling for violence and killing," Khalaf said, adding that security forces had been dispatched to enforce the closure orders.
Within hours, the two channels were showing a message saying that they had been closed by order of the government.
A journalist at Salah al-Deen said Iraqi security forces had come to the office and ordered them to stop broadcasting.
The government has previously complained about channels it says are fomenting sectarian conflict. It bans pan-Arab news station Al Jazeera and forced its main rival, Al-Arabiya, to shut its Baghdad bureau for a month in September.