Israel has targeted one of Syria's positions in Hama province, which a war monitor says was a branch of the government agency accused by the US of producing chemical weapons.
The army statement said on Thursday the air strike 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 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 said seven people were killed and wounded in the strike.
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.
The Israeli army declined to comment.