A spokesman for the U.N. Relief and Works Agency told the BBC as many as 10,000 refugees are fleeing the area following the reported deaths of 30 people in three days of military action.
The report came amid a crackdown in Damascus and warnings from Turkey that military action against protesters must stop.
Violence across Syria claimed at least 42 lives Sunday, an anti-government group told CNN.
Among the dead in Latakia were three children and two soldiers, said the Local Coordination Committees of Syria, a network of opposition activists operating inside the country.
Syrian President Bashar Assad -- and his troops -- blamed the violence on outsiders meddling in the country's business.
"The terrorists were using arms and dynamite," said Ayman Kasser, a government soldier. He said he was shot in the leg when gunmen attacked his unit.
"The regime smashed the city [Latakia] in April, and now it's re-entering to arrest protesters in the poor regions," said an activist who gave his name as Ammar. "The regime declared then that it was finishing off 'armed gangs.' What will it say now?"
The months-long unrest in Syria calling for Assad's ouster left as many as 2,000 civilians dead, observers have estimated.