Five rebels were killed, the state-run Syrian Arab News Agency (Sana) reported on Saturday.
Sana, quoting an unnamed official at the Syrian Interior Ministry, said the clash took place on Friday night in the province of Hama and that the rebels belonged to the Jund al-Sham organisation.
None of the rebels survived, the agency said.
It said the clash began when anti-terrorism forces raided the group's hideout - an isolated house in the village of Jibrin.
Police seized weapons, bombs and explosives at the house, it added.
The ministry official said the group was planning to carry out "terrorist" operations and destabilise security in the country.
Jund al-Sham, whose Arabic name means Soldiers of Syria, is a well-known organisation that was set up in Afghanistan by Syrian, Palestinian and Jordanian groups, and has links to Abu Musab al-Zarqawi, the head of al-Qaida in Iraq.
Syrian authorities have been monitoring Jund al-Sham for months and have clashed recently with members of the group which it said were planning to launch bomb attacks in Damascus.
Syria, a tightly controlled country, has for decades taken a tough line against what it calls extremism.
In 1982, members of the Muslim Brotherhood staged a rebellion in Hama.
During the ensuing clashes, Syrian forces razed much of the city, killing as many as 10,000 people and finally crushing the Brotherhood after a five-year war.