At least three people were killed and property damaged when Israeli warplanes struck near the Syrian capital, Damascus, the defense ministry said.
Earlier, the official SANA news agency reported that Syria’s air defenses had intercepted Israeli missiles.
Correspondents of the French News Agency (AFP) in Damascus reported that they heard loud explosions.
According to the Syrian Observatory for Human Rights, the missiles targeted Iranian bases near the Syrian capital.
An Israeli rocket attack on May 14 killed five soldiers.
Since the start of the war in Syria in 2011, Israel has launched hundreds of airstrikes on its neighbor, targeting positions of the Syrian army, Iranian forces and Lebanese Hezbollah.
Israel rarely comments on its attacks on Syria, but has repeatedly stressed that it will not allow Iran to expand its influence in Syria.
Sparked by the crackdown on pro-democracy protests, the war in Syria has claimed the lives of some 500,000 people, destroyed the country’s infrastructure and displaced millions.