Syria's army said Israel targeted one of its positions in Hama province early on Thursday, which a war monitor said was a branch of the government agency accused by the US of producing chemical weapons.
The army statement said the airstrike killed two people and caused material damage near the town of Masyaf and warned against the "dangerous repercussions of this aggressive action to the security and stability of the region".
The war monitor, the Syrian Observatory for Human Rights, said the strikes hit a Scientific Studies and Research Centre facility, the agency the US describes as Syria's chemical weapons manufacturer.
The Observatory also said that a military storage camp next to the centre was used to store ground-to-ground rockets and that personnel of Iran and its allied Lebanese Hezbollah group had been seen there more than once.
It gave the total number of dead and wounded in the strike as seven.
Israeli officials have in the past admitted that Israel has attacked weapons shipments bound for Lebanon's Iran-backed Hezbollah group, an ally of Syrian President Bashar al-Assad, without specifying which ones.
An Israeli army spokeswoman declined to discuss reports of a strike in Syria, saying the army does not comment on operational matters.
Amos Yadlin, a former head of Israeli military intelligence, tweeted that the reported attack was not routine and targeted a Syrian military scientific centre.
"The facility at Masyaf also produces chemical weapons and explosive barrels that have killed thousands of Syrian civilians," Yadlin said in the tweet.
There was no independent confirmation that this was the target but the United Nations has said in the past that the Syrian government has carried out chemical weapons attacks, which Damascus denies.
Israeli officials have also previously said that Israel and Russia, another Assad ally, maintain regular contacts to coordinate military action in Syria.
Jets flying over Lebanon overnight broke the sound barrier and Lebanese media reported that some Israeli jets had breached Lebanese airspace.