Syria’s army said Israeli jets had targeted a military research centre north-west of Damascus on Wednesday, killing two people and wounding five.
It denied reports that lorries carrying weapons bound for Lebanon were hit.
Russia has called the attack unacceptable, while a Syrian official and Iranian deputy minister have suggested there could be retaliation.
The Syrian army statement about the incident, carried on state media, said Israeli fighter jets had carried out a direct strike on a scientific research centre in Jamraya.
Meanwhile Lebanese security sources, Western diplomats and Syrian rebels say an arms convoy near Lebanon’s border was targeted. A US official attested to the strike, saying the lorries were carrying Russian-made SA-17 anti-aircraft missiles.
Israel has declined to comment.
The latest developments have struck a country in turmoil. Syrian President Bashar al-Assad continues to cling to power despite a 22-month conflict that has killed more than 60,000 people.
Syria’s foreign ministry summoned the UN commander in the Golan to deliver its formal protest, saying Israel’s action violated the 1974 disengagement agreement between the two sides, who remain technically at war.
A UN observer force has been in place in the Golan since 1974, with the task of providing “an area of separation and for two equal zones of limited forces and armaments on both sides of the area”.
An Israeli air strike on Syria could cause a major diplomatic incident, analysts say, as Iran has said it will treat any Israeli attack on its ally Syria as an attack on itself.
Iran’s foreign minister condemned the alleged air strike as an “overt assault based on the West’s policy” to undermine stability in Syria.
“The Zionists got ahead of themselves in trying to cover up the successes of the Syrian government and nation in maintaining the existing government and restoring stability and security,” Ali Akbar Salehi was quoted as saying by the semi-official ISNA news agency.
Iran’s Fars news agency quoted the Deputy Foreign Minister Hossein Amir Abdollahian as saying the raid would have “grave consequences for [the major Israeli city of] Tel Aviv”.
Syrian Ambassador to Lebanon Ali Abdul-Karim Ali said Damascus could take a “surprise” decision to retaliate.
The Russian Foreign Ministry said: “If this information is confirmed, then we are dealing with unprovoked attacks on targets on the territory of a sovereign country, which blatantly violates the UN Charter and is unacceptable, no matter the motives to justify it.”
Relations between Russia and Israel have been improving in recent years as trade and economic ties have grown stronger, says the BBC’s Steve Rosenberg in Moscow.
But Moscow is a close ally of President Assad, which would explain its concern at the reports, our correspondent adds.
The Syrian army statement said the Jamraya centre – which was focused on “raising our level of resistance and self-defence” – was damaged in the attack, and specifically denied reports that an arms convoy had been hit.
It said “armed terrorist gangs” – a term the government uses to describe rebel groups – had tried and failed repeatedly to capture the same facility in recent months.
Some reports suggest the facility could be Syria’s Scientific Studies and Research Centre, known by its French acronym CERS, believed to be the state organisation responsible for developing biological and chemical weapons.
The Lebanese military and internal security forces have not confirmed the reports of an attack on an arms convoy.
But they say there has been increased activity by Israeli warplanes over Lebanon in the past week, and particularly on Tuesday and the early hours of Wednesday morning.
Israel has voiced fears that Syrian missiles and chemical weapons could fall into the hands of militants such as the Lebanese Shia militant group, Hezbollah.
Correspondents say Israel is also concerned that Hezbollah could obtain anti-tank and anti-aircraft missiles, thus strengthening its ability to respond to Israeli air strikes.
Israel believes Syria received a battery of SA-17s from Russia after an alleged Israeli air strike in 2007 that destroyed a Syrian nuclear reactor near Deir Ezzor in eastern Syria, analysts say.
The US government said in 2008 that the reactor was “not intended for peaceful purposes”.
Hezbollah said Wednesday’s target was the Jamraya centre, condemning the attack as “an attempt to thwart Arab military capabilities” and pledging to stand by its ally Mr Assad.
The reported attack came days after Israel moved its Iron Dome defence system to the north of the country.
Israel has also joined the US in expressing concern that Syria’s presumed chemical weapons stockpile could be taken over by militant groups.