Syrian air defenses identified a missile that was fired towards the city of Masyaf near Hama late on Thursday and destroyed it before it hit its target, a Syrian military source said.
Several attacks, some of which attributed to Israel, have been reported in the past in this part of Syria, which has some Iranian military bases and a missile development facility.
The missile was fired from the direction of northern Lebanon, the military source added in a statement distributed on a messaging app.
State television had previously reported the sound of a massive blast near Masyaf in Hama province although there were no immediate reports of damage or casualties.
A spokeswoman for Israel's military declined to comment on the strike, but Israel has acknowledged repeatedly striking targets inside Syria in recent years. Some attacks Damascus has attributed to Israel have been made from Lebanese airspace.
Israel wants to stop military build-up in Syria by its arch regional foe Iran and Tehran's close military ally the Lebanese Hezbollah group, which are both fighting on President Bashar al-Assad's side in Syria's eight-year civil war.