Syrian state television has reported that Israeli rockets have hit Jamraya army research centre near Damascus.
Witnesses heard huge explosions near the Jamraya facility, and residents said 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 neighboring 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 said 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.
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.
More than 70,000 people are estimated to have been killed since the conflict erupted in March 2011.