Syrian air defenses identified a missile that was fired toward the city of Masyaf near Hama late Thursday night and destroyed it before it hit its target, a Syrian military source said.
The missile was fired from the direction of northern Lebanon, the military source added in a statement that was distributed on a messaging app.
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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.
Arab media outlets reported heavy explosions at a military facility, which was believed to be a weapons storehouse used by pro-Iranian militias. One report said that Iranian missiles had been moved to the facility via Iraq.
An IDF spokeswoman declined to comment on the strike, but Israel has acknowledged repeatedly striking targets inside Syria in recent years. Some attacks that 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 terrorist group, Hezbollah, which are both fighting on the side of Syrian President Bashar Assad in Syria's eight-year war.