The Foreign Ministry asked the Security Council to take "strict and immediate" measures to stop such Israeli attacks, in a statement carried on the state-run SANA news agency.
Wednesday's strike hit a copper factory in the industrial town of Hisya, 35 km (21 miles) south of Homs and 112 km north of Damascus, SANA reported.
The Al-Mayadeen channel, closely associated with the Assad regime, reported the attack targeted a security facility in an industrial zone in a Homs suburb. They also reported Syrian forces responded with surface-to-air missiles.
The Lebanese Anshara website reported huge explosions near the villages of al-Eyn al-Jedida, located in the eastern mountain range on the Lebanon-Syria border. Local residents reported Israeli jets circling the area prior to the explosion.
Sky News' Arabic edition reported four strikes on the facility, which allegedly doubled as a weapons depot. Hezbollah's Al-Manar TV reported Israeli jets circling the area for over an hour.
In Jerusalem, Israel's Foreign Ministry declined to comment. On Wednesday, Israel's Channel 10 said the aircraft were not hit and returned safely to base.
The Israeli air force says it has struck arms convoys of the Syrian military and its Lebanese ally, the Iran-backed Hezbollah, nearly 100 times in recent years.
Israeli officials have expressed alarm at Iranian influence in Syria, where Iran-backed groups have played a critical role fighting in support of President Bashar al-Assad during the conflict that erupted in 2011
Last month, Israel attacked an anti-aircraft battery after it fired a missile targeting Israel Air Force Planes.
The Syrian military warned of "dangerous consequences" following the rare strike, claiming that they successfully hit an Israeli jet during the strike. Prime Minister Benjamin Netanyahu responded to the strike, saying that "today they attempted to hit our planes," calling the incident "unacceptable." He added that "if anyone attempts to harm us, we will harm them back."
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