The airstrike targeted a facility near the town of Masyaf, in Hama province, described by some as a missile producing factory, amid Israeli outrage over Iran's growing influence in the war-torn country.
Other reports suggested the facility was tied to Syria's chemical weapons program.
In a statement, the Syrian army said the Israeli warplanes fired several missiles from Lebanese air space, and warned of the "dangerous repercussions of such hostile acts on the security and stability of the region."
He said Israel isn't "looking for adventures, and we don't want to be dragged into this fight or another."
"We are determined to prevent our enemies from harming or even creating the possibility of harming the security of Israeli citizens."
Israel has carried out several airstrikes against suspected arms shipments it believed to be bound for Lebanon's Hezbollah militant group, which is fighting alongside President Bashar Assad's forces, over the course of Syria's civil war, now in its seventh year.
The airstrike comes amid heightened tensions over Iran's growing reach in Syria. Israel's Prime Minister Benjamin Netanyahu claimed recently that Iran is building sites in Syria and Lebanon for the manufacture of "precision-guided missiles" with the aim of deploying them against Israel.
Today's air raid was seen as a message to both Russia and Iran that Israel can strike anywhere in Syria.
This week, Israel is conducting a massive drill along its border with Lebanon simulating war with the Iranian-backed Hezbollah.
Rami Abdurrahman, who heads the Britain-based Syrian Observatory for Human Rights, said two facilities were hit in today's airstrike, a scientific research center and a nearby military base where short-range surface-to-surface missiles are stored.
"Many explosions were heard in the area after the air raid," said Abdurrahman, whose group relies on a network of activists across the country.
He said Lebanese Hezbollah fighters and Iranian military officials often visit the site, adding that those killed and wounded were Syrians.
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