It said the Israeli assault also wounded five people.
The SSRC is promoted as a civilian research institute by the Syrian government but the USA accuses the agency of focusing on the development of non-conventional weapons and the means to deliver them. The site also is believed to house a chemical weapons factory.
The Observatory said strikes also hit a military storage camp next to the center that was used to store ground-to-ground rockets and where personnel of Iran and its allied Lebanese Hezbollah group had been seen a couple of times.
Israel has long warned that the weapons from Iran and Syria reach to the hands of Hezbollah, Israel's arch enemy.
Israel said later it would not allow the transfer of weapons from Syria to Hezbollah.
While he refused to confirm that Israel carried out the airstrikes, he said that if it did, it would show "Israel intends to enforce its readiness despite the fact that the great powers are ignoring them".
"If Israel strikes Hezbollah in Lebanon, definitely it will respond", the official said. Both have suggested that any new conflict between them could be on a larger scale than that one.
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Israeli warplanes have reportedly pounded a chemical weapons facility belonging to the Syrian regime headed by President Bashar al-Assad.
A month before, Israel bombed a military airport near Damacus.
That attack prompted the USA to launch air and missile strikes against the Syrian government.
The air raid was reported to have occurred overnight, on the Syrian Scientific Studies and Research Centre near Hama. He gave no details but warned "this is something Israel can not accept".
Unconfirmed Arab media reports say a chemical weapons production facility was hit in the attack.
The attack killed at least 87 people and prompted the United States to launch a cruise missile strike on a Syrian military airport where it said the attack had originated.