"Just in the last 36 hours did the [Israel Air Force] attack Iranian warehouses with Iranian weapons at the global airport in Damascus", the premier said.
Syrian air defences shot down most of the "hostile" missiles, though one hit a warehouse at Damascus International Airport, SANA news agency said.
Syria on Friday claimed that Israel has filed multiple missiles towards Damascus which triggered Syrian air defences that shot down a lot of them.
Netanyahuy said the Israel Defense Forces has attacked hundreds of Iranian and Hezbollah targets.
Syria's aviation ministry said that operations at the Damascus airport were unaffected by the attacks, and that flights continued normally throughout the night.
The Syrian Foreign Ministry said on Saturday that the Israeli actions in Syria are no different from those of Islamic State (IS) militants, state news agency SANA reported.
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The Israeli jets reportedly crossed over to Syria through Lebanese airspace after having heavily roamed over Lebanon on Thursday.
Only a warehouse in the Damascus International Airport was damaged, according to the statement. However, the Arab country's air defense systems have thwarted most of the attacks.
Prime Minister Benjamin Netanyahu said Sunday that Israel had at the weekend carried out an air strike on Iranian weapons in Syria, a rare public confirmation of such attacks.
Russian Federation is a main ally of Damascus.
"Our air defenses immediately responded to the hostile missiles and shot down majority", the source said.
It was the first airstrike on the Damascus area this year since Israeli warplanes struck areas near the capital at the end of December.