Israeli rockets have hit an army research centre near Damascus, Syrian state TV has reported.
Witnesses heard huge explosions near the Jamraya facility, and residents told the BBC that nearby military positions were also hit.
The Jamraya site was the target of an Israeli strike in January.
Earlier, unnamed Israeli officials said that on Friday Israeli aircraft had attacked a shipment of missiles inside Syria.
The missiles were believed to be destined for Hezbollah militants in neighbouring Lebanon.
The latest attacks come amid reports of massacres in a campaign of sectarian cleansing near the coastal region of central Syria.
Heavy explosions shook Damascus overnight. Amateur footage posted online claimed to show the blasts at the Jamraya research centre, on Mount Qassioun overlooking Damascus.
Residents told the BBC that military bases in the area had also been hit.
Syrian state media said the attack showed that there was an organic link between Israel and the rebels.
“The new Israeli attack is an attempt to raise the morale of the terrorist groups, which have been reeling from strikes by our noble army,” state TV said, referring to recent offensives by President Bashar al-Assad’s forces.
Damascus-based journalist Alaa Ebrahim told the BBC it was “the biggest explosion” the city had seen since the conflict began two years ago.
He said residents living near Jamraya reported feeling a “mild earthquake” just before the blast, indicating that the rockets may have hit an underground facility.
He added that the Syrian army was likely to have suffered major casualties in the attack.
The UK-based Syrian Observatory for Human Rights quoted eyewitnesses in the area as saying they saw jets in the sky at the time of the explosions.
There was no immediate comment from Israeli officials on the latest explosions.
Israeli officials have confirmed their forces have carried out two air strikes on Syrian targets this year.
The first attack, in January, apparently targeted the Jamraya facility.
The second, two days ago, targeted a consignment of missiles bound for Lebanon’s Hezbollah.
In a separate development, hundreds of Syrian families have fled the coastal area of central Syria amid reports of massacres.
Activists said that more than 100 people, including women and children, were killed in the Sunni village of al-Bayda and the nearby coastal town of Baniyas.
There was fighting in the area before al-Bayda was overrun by government forces and the Alawite shabiha militia on Thursday.
The BBC’s Jim Muir in neighbouring Lebanon says there was a strong sectarian dimension to the reported actions.
Alawites, who make up about 10% of the Syrian population, have largely stayed loyal to Mr Assad.
The government said it had pushed back “terrorist groups” and restored security to the area.
The US said it was “appalled by the horrific reports” but that it did not foresee sending US troops to tackle Syria’s civil war.
US President Barack Obama reaffirmed on Friday that clear evidence of chemical weapons would be a “game changer”, but that any response would not be rushed.
However his administration is no longer ruling out supplying weapons to the rebels.
Syrian troops and opposition forces have been fighting around Damascus for months, but neither side has gained the upper hand.
More than 70,000 people are estimated to have been killed since the conflict erupted in March 2011.