Syrian air defense systems intercepted Sunday a missile attack "from the occupied lands," state news agency SANA reported.
On Monday, The British-based Syrian Observatory for Human Rights said at least three non-Syrian nationals were killed in the strike.
According to the report, the alleged Israeli attack took place in the Damascus area. One "hostile target" was downed near Aqraba, southeast of the capital, SANA added.
Four cruise missiles were believed to have been launched across the coast through Lebanese airspace towards Syria, a source in the regional alliance supporting Syrian President Bashar al-Assad told Reuters.
The Britain-based Syrian Observatory for Human Rights, an opposition war monitoring group that has activists around the country, said the missile attack targeted Iranian and Syrian military positions near Damascus.
Residents of Damascus said explosions could be heard near the capital.
In neighboring Lebanon, Israeli warplanes could be heard flying in the country's airspace at the time of the airstrikes in Syria. Damascus had said in the past that Israeli warplanes have fired missiles into Syria from Lebanon's airspace.
There was no immediate comment from Israel.
Israel has repeatedly struck Iran-linked targets in Syria in recent years, including supplies sent by pro-Iranian Lebanese Hezbollah to support Assad's forces, and has warned against any permanent Iranian presence on the frontier.
Iran and Hezbollah are fighting on Assad's side in the Syrian war, and Israel says they are trying to turn Syria into a new front against Israelis.
Israel has vowed it will continue its strikes against Iranian targets trying to establish a permanent military presence there and against advanced weapons shipments to Hezbollah.
In November, Israel killed a senior commander of the Palestinian Islamic Jihad, an Iran-backed group in the Gaza Strip, setting off two days of heavy fighting. A separate airstrike targeted but failed to kill an Islamic Jihad leader in Damascus, underscoring the risk of escalation at various pressure points across the volatile region.
Reuters contributed to this report.