The Syrian military says Israeli jets have carried out an air strike on its territory, but denied reports that lorries carrying weapons bound for Lebanon were hit.
It said in a statement that the target was a military research centre northwest of the capital Damascus.
Two people were killed and five injured in the attack, it said.
Lebanese security sources, Western diplomats and Syrian rebels say an arms convoy was hit near Lebanon's border.
The attack came as Israel voiced fears that Syrian missiles and chemical weapons could fall into the hands of militants such as Lebanon's Hezbollah.
On Thursday, Russia's foreign ministry expressed "grave concerns" over the alleged Israeli attacks.
"If this information is confirmed, then we are dealing with unprovoked strikes at targets on the territory of a sovereign state, which grossly violates the UN Charter and is unacceptable, whatever motives are used to justify it," the statement said.
BBC Middle East correspondent Wyre Davies says none of the reports can be verified, although some well-placed diplomats and military sources say they would not be surprised if Israel had acted, given the recent instability in Syria.
Israel and the US have declined to comment on the incident.
The Lebanese military and internal security forces have not officially confirmed the reports, but say there has been increased activity by Israeli warplanes over Lebanon in the past week, and particularly in recent hours.
The army statement, quoted in Syria's official media, said: "Israeli fighter jets violated our airspace at dawn today and carried out a direct strike on a scientific research centre in charge of raising our level of resistance and self-defence."
The centre, in Jamraya, northwest of the capital Damascus, was damaged in the attack, along with an adjacent building and a car park, the statement said.
It said that "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.
The statement specifically denied reports that an arms convoy had been hit.
The Jerusalem Post said the description of the facility fitted that of Syria's Scientific Studies and Research Centre, believed to be the state organisation responsible for developing biological and chemical weapons.
Hours earlier, unnamed Lebanese security sources reported that Israeli warplanes had struck lorries carrying missiles towards the Lebanese border
The Associated Press quoted a US official as saying the lorries were carrying Russian-made SA-17 anti-aircraft missiles.
Correspondents say Israel fears that Lebanese Shia militant group Hezbollah could obtain anti-tank and anti-aircraft missiles, thus strengthening its ability to respond to Israeli air strikes.
However, an attack on the Syrian side could cause a major diplomatic incident, they say, as Iran has said it will treat any Israeli attack on Syria as an attack on itself.
The 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, although there is no evidence that the convoy was carrying such weapons.
Analysts say 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.
The US government said in 2008 that the reactor was "not intended for peaceful purposes".