Israel's Minister of Intelligence said the strike was consistent with policy regarding the transfer of weapons
The Kremlin on Thursday called for restraint after Syria accused Israel of firing several missiles at a military position near the Damascus airport.
"We continue to consider that all countries need to refrain from any kind of actions that lead to an increase in tension in this already restive region and call for respect of the sovereignty of Syria," Kremlin spokesman Dmitry Peskov told reporters.
Russia, which has deployed its forces to back up the Syrian regime, has a hotline set up to avoid clashes with Israeli jets in the skies over the war-torn country.
Peskov did not confirm if Israel had warned Moscow of the strike, saying only that the two nations' "defence ministries are in constant dialogue".
Russian foreign ministry spokeswoman Maria Zakharova later went further than the Kremlin and slammed the alleged Israeli strikes.
"Gross violations of Syrian sovereignty -- no matter how they are justified are unacceptable," she said in a televised briefing.
"Moscow condemns acts of aggression against Syria."
In line with its usual practice, Israel's military declined to comment on the latest blast, which saw a huge explosion near Damascus.
Syrian state media earlier on Thursday accused Israel of carrying out the huge blast which struck near Damascus airport in the early morning hours.
"A military position southwest of Damascus International Airport was targeted at dawn today by an Israeli aggression using several missiles fired from occupied territory, sparking explosions in the area," the SANA news agency said, citing a military source.
Earlier, Israel's Minister of Intelligence Israel Katz seemed to hint that this could be the case, telling Army Radio that the strike was consistent with Israeli policy regarding the transfer of weapons to Hezbollah.
There was an explosion at weapons and fuel depots belonging to Assad regime forces and Iranian-linked militia, the Hezbollah-affiliated Al-Manar news network reported. There were no reports of any injuries.
Reports circulating in Arab media claimed that the Israeli air force hit the location five times at around 5am local time, targeting weapons that were arriving for Iranian-backed militant groups.
According to the Syrian Observatory for Human Rights, a London-based monitoring group, the explosions caused a fire.
"The blast was huge and could be heard in Damascus," said Rami Abdel Rahman, head of the group.
The Damascus International Airport lies about 25 kilometers southeast of Syria's capital.
The Observatory, which gathers information from sources across war-ravaged Syria, said it had confirmed the explosion had not taken place inside the airport itself.
"It's unclear what caused the explosion, but there fires raging at the site," Abdel Rahman said.
In January a series of explosions ripped through the al-Mazzeh military airport on the western outskirts of Damascus. Syrian media was quick to attribute the airstrikes to the Israel Defense Forces. State news agency SANA said Israel had launched the missiles from Israeli territory north of the Sea of Galilee.
On Friday the military said that it had hit targets in Syria in response to three projectiles that landed in the Israeli Golan Heights earlier, in what the army said was likely stray fire from Syria's civil war. There were no injuries or damage.