"Syria has given the green light to set up missile batteries to directly attack Israeli targets," Raja said.
The comments by the Popular Front, which has its power base among the Palestinian refugee camps of Syria, came as John Kerry, the US Secretary of State, held talks in Russia in an attempt to find "common ground" on Damascus.
The US and Russia said they will convene a new international conference later this month to build on a transition plan they set out last year in Geneva.
Kerry said the plan should be a road map for peace and not just a "piece of paper". The goal is still to bring the Assad regime and representatives from the opposition together for talks on setting up an interim government, Kerry said.
The Popular Front, which began life as a Syrian-backed Palestinian splinter faction in 1968, has a long history of attacking Israeli targets, killing 47 people during the bombing of a Tel Aviv-bound Swissair plane in 1970.
In 1987, a guerrilla from the militant group flew from Lebanon into Israel on a hang-glider and killed six soldiers before being shot dead.
Unlike some other Palestinian factions based in Syria, who have turned against the Government in protest over its suppression of the democratic uprising, it has remained strictly loyal to Assad.
In practice, it is a relatively minor player compared with other Islamic militant factions such as Hamas and Hizbollah. However, the prospect of Palestinian factions attacking Israel from bases outside its borders will evoke worrying comparisons with Israel's conflict with Lebanon in the 1980s, and would complicate any future peace deal.
Yesterday, the conflict in Syria escalated, mostly around the Golan Heights, a traditional flashpoint with neighbouring Israel. A group of Syrian rebels calling itself the Yarmouk Martyrs Brigades abducted four United Nations peacekeepers patrolling the area, accusing them of shielding soldiers who had killed civilians in the southern town of Wadi Raqat.
The group insisted that the four Filipino peacekeepers were being detained for their own safety, but Ban Ki Moon, the UN Secretary-General, called for their immediate release.
Israel's Defence Minister, Moshe Yaalon, warned that Israeli troops stationed around the Golan Heights would return fire if shelling from the Syrian side continued.
- Additional reporting, AP