Syrian regime media has said missiles came from the Israeli-occupied Golan heights while a war monitor said another four have been injured after the strikes.
Israeli surface-to-surface missiles killed three people near the Syrian capital Damascus on Friday, regime media said quoting a military source.
"The Israeli enemy carried out an aggression ... that led to the death of three martyrs and some material losses," Syria's SANA news agency quoted the source as saying.
The missiles came from the Israeli-occupied Golan Heights and were intercepted by the Syrian air defences, the military source said.
AFP correspondents in the Syrian capital said they heard very loud noises in the evening.
The Syrian Observatory for Human Rights war monitor said that the three people killed were officers and that four other members of the air defence crew were wounded.
The Israeli strikes targeted Iranian positions and weapon depots near Damascus, the monitor said.
A fire broke out at one of the positions near the Damascus airport, where ambulances were seen rushing to the site of the strikes, according to the Observatory.
READ MORE: Israel kills, wounds many in Syria
Targeting Hezbollah, affiliates
The latest strike follows one on May 13 that killed five people in central Syria, and another one near Damascus on April 27 which, according to the Observatory, killed 10 combatants, among them six Syrian regime soldiers, in the deadliest such raid since the start of 2022.
Since civil war broke out in Syria in 2011, Israel has carried out hundreds of air strikes there, targeting regime troops as well as allied Iran-backed forces and fighters of Hezbollah.
While Israel rarely comments on individual strikes, it has acknowledged carrying out hundreds of them.
The Israeli military has defended them as necessary to prevent its arch-foe Iran from gaining a foothold on its doorstep.
The conflict in Syria has killed nearly half a million people and forced around half of the country's pre-war population from their homes.