Syrian state media said loud blasts coming from an air base early on Sunday were from an explosion at an ammunitions dump caused by an electrical problem, but an official in the regional alliance backing Damascus said they were from Israeli strikes.
A group monitoring the Syrian war says at least two military personnel were killed and 11 wounded in the overnight explosions.
The state media cited a military source as saying there was no "Israeli aggression" directed at the Mezzeh airbase near Damascus, after the sound of explosions was heard across the Syrian capital.
Iran's state news agency IRNA quoted an unnamed Iranian military official based in Syria as saying that the blast was caused by "an electrical short-circuit in an ammunition depot" on the outskirts of Damascus.
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A war monitor, the Syrian Observatory for Human Rights, also attributed the blasts to Israeli strikes, which it said caused deaths and injuries.
Israel has previously acknowledged having carried out air strikes in Syria aimed at degrading the capacity of Iran and its allies, including Lebanon's Shi'ite Hezbollah group, which are backing Assad in the country's seven-year civil war.
There was no immediate comment from Israel on reports of Sunday's blasts or that it was behind them.
In May, it said it attacked nearly all of Iran's military infrastructure in Syria after Iranian forces fired rockets at Israeli-held territory for the first time in the most extensive military exchange ever between the two adversaries.
Mezzeh airbase was bombed several times over the last few years, with some of the strikes being attributed to Israel. This due to the claim the base houses weapon storage facilities used by Iran and Hezbollah.