In an earlier report, SANA had spoken of Syrian air-defense batteries attacking "enemy targets".
Syrian air defenses came to life around the Damascus airport on Friday night, as Israeli warplanes carried out attacks in the area.
The Britain-based Syrian Observatory for Human Rights said at least two Israeli rockets hit the outskirts of the airport.
A Transport Ministry spokesperson told SANA that air traffic from the airport was unaffected by the conflict.
"Only a ministry of transport warehouse at Damascus worldwide airport was hit", SANA cited the military source as saying.
The Israeli jets reportedly crossed over to Syria through Lebanese airspace after having heavily roamed over Lebanon on Thursday.
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On December 25 a similar strike near the capital Damascus wounded three Syrian soldiers.
An unidentified Syrian official was quoted by state media as saying Israeli aircraft coming from the south fired several missiles at areas near Damascus about 45 minutes before midnight on Friday.
The ministry made the remarks in its letters to the United Nations about the Israeli missile attack on Syrian military sites in the capital Damascus on Friday. However, the Arab country's air defense systems have thwarted most of the attacks.
Russian Federation is a main ally of Damascus. While Israeli sources claimed that the positions were being used by Iranian forces, the airstrikes injured several Syrian service members.