Israel has carried out almost 100 strikes in Syria since the beginning of the civil war there - many against convoys attempting to transfer precision weapons to Hezbollah, the country's air force chief told local media last month.
The attack came from Lebanese airspace.
The Syrian Foreign Ministry filed a complaint to the United Nations Security Council and the Secretary General on Thursday, following the earlier strike it blamed on Israel.
A few hours after the attack, the Syrian Army warned that there will be "dangerous repercussions", calling the airstrike an aggressive move that threatens the "security and stability in the region". Syria denies having or using chemical weapons.
Prof Moshe Maoz, an expert in Israeli-Syrian relations, told Tazpit Press Service that "the strike was a sign to Putin after the meeting in Sochi, where the two didn't agree on a strategy toward Syria".
The SSRC is promoted as a civilian research institute by the Syrian government but the United States accuses the agency of focusing on the development of non-conventional weapons and the means to deliver them.
Amos Yadlin, a former head of Israeli military intelligence, wrote that the reported attack was not routine and targeted a Syrian military scientific center.
The Israeli Army has declined to comment on the incident, according to Reuters, as it does not comment on operational matters..
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The SSRC oversees advanced missile production and remaining stockpiles of chemical weapons, including sarin gas.
Nor has Hezbollah, with the notable exception of a 2015 anti-tank missile attack on an IDF jeep that killed two soldiers, though that was in response to an alleged Israeli strike that killed the arch-terrorist Samir Kuntar, not an attack on a weapons convoy or warehouse.
The air raid was reported to have occurred overnight, on the Syrian Scientific Studies and Research Centre near Hama.
The alleged IAF strikes come amid rising tensions between Israel, the USA, and Russian Federation regarding Iran's expanding military presence in Lebanon and Syria, partly through its terrorist proxy Hezbollah.
In the past several years, Israeli military has carried out sporadic attacks against various targets across Syria.
Hezbollah has been one of Syrian President Bashar al-Assad's most important allies in the war and last month its leader Sayyed Hassan Nasrallah said he had recently travelled to Damascus to meet the Syrian president.
Hezbollah and Israel fought a brief war in 2006 in which more than 1,300 people died. It was not clear if there were casualties among Iranian and Hezbollah operatives.
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Merkel responded: "We had a very dramatic situation then.There are times in the life of a chancellor when she has to decide". Brussels, which has already frozen Turkey's entry negotiations, is now likely to consider further actions.