Syria's government says unrest in the country's third-largest city, Homs, and in the northern city of Baniyas amounts to an armed insurrection.
The warning came after thousands of demonstrators occupied the centre of Homs on Monday, vowing to stay until the president was ousted.
Witnesses say security forces fired on the protesters in Homs and there are reports the square was cleared.
Rights activists say about 200 Syrians have been killed in weeks of unrest.
President Bashar al-Assad announced on Saturday he would end nearly half a century of emergency rule next week, while the authorities have also been releasing political prisoners, both key demands of protesters.
But Syria's unprecedented wave of unrest shows no sign of abating, says the BBC's Kim Ghattas in Beirut, in neighbouring Lebanon.
In a statement late on Monday, the interior ministry said: "The course of the previous events... have revealed they are an armed insurrection by armed groups belonging to Salafist organisations, especially in Homs and Baniyas."
It warned "their terrorist activities will not be tolerated".
Salafism is a strict form of Sunni Islam which many Arab governments equate with militant groups like al-Qaeda.
Our correspondent says this means the authorities will crack down on dissent under the pretext of fighting terrorists.
At least 5,000 demonstrators occupied Clock Square in Homs on Monday after mass funerals for about 12 protesters slain by security forces at the weekend.
Checkpoints were set up around the square to ensure people coming in were unarmed civilians, and protesters stocked up on supplies.
One protester said it had been renamed Tahrir Square, after the one in Cairo which was the focal point of the uprising that toppled Egyptian President Hosni Mubarak.
Witnesses said that security forces told them through loud-hailers to leave, before firing tear gas, then live ammunition.
One protester, Omar, told BBC Arabic on Tuesday that he had seen one person shot dead.
"Listen to the shooting," he said, "Can you hear it? It's hammering on us like rain.
"Security forces... listen to the shooting, where is it coming from? It can't be coming from thugs, it's so heavy."
An activist in the capital Damascus told AFP news agency by telephone: "The sit-in was dispersed with force. There was heavy gunfire."
The official Sana news agency has also been reporting on events in Homs.
It said three army officers, including a brigadier-general, together with his two sons and a nephew, were killed on Sunday by "armed criminal gangs", which then mutilated the bodies.
The northern town of Baniyas also saw anti-government protests on Sunday.
Demonstrations against the authoritarian rule of Mr Assad's Baath Party spread after breaking out in the southern city of Deraa in mid-March.
The unrest poses the gravest threat to his rule since he succeeded his father Hafez al-Assad 11 years ago.