The Lebanese government is also expected to lodge a complaint against Israel at the United Nations in the coming days for allegedly using its airspace to carry out the strikes.
Syria's state TV says that Israeli warplanes launched an attack in central Syria overnight and that Syrian air defenses hit back.
The Israeli air force says it has struck arms convoys of the Syrian military and its Lebanese ally, the Iran-backed Hezbollah, almost 100 times in recent years.
The Israeli attack is the latest in a string of similar moves that have targeted Syrian military posts on the pretext that the targeted areas contain Hezbollah-bound weapons.
The Syrian Observatory for Human Rights, a UK-based monitoring group, reported that the strike targeted a Syrian military or Hizbullah installation that was believed to manufacture rockets.More news: Whole Foods Market to add 6000 workers during hiring event
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Lebanese President Michel Aoun warned on Thursday that the entire country is "prepared to fight Israel", following a reported Israeli attack on Hezbollah targets in Syria that from Lebanese airspace.
According to the Israeli army spokesperson, the Israeli planes were in fact on a reconnaissance mission in Lebanon to photograph sites for Israeli intelligence. He also said that an anti-aircraft missile was sacked by Syrian forces.
There was no immediate comment from Israel.
Israel and Syria have exchanged fire on numerous occasions in recent months.