According to Lebanese media, the strike was executed from Lebanon's territory.
The Hezbollah-affiliated Al Mayadeen network reported that the alleged targets were scientific research centers for chemical arms production.
The newsflash did not elaborate on what exactly had been targeted. An intelligence source said a major military research center for chemical arms production was located near the city.
A Syrian military source said that "one of the military sites near Misyaf was attacked by the Israeli Air Force (IAF)," according to the SANA news agency.
The source added that only damage to property was caused, and no casualties were immediately reported.
However, Syrian opposition members reported that Iran's Revolutionary Guards as well as Hezbollah's members were killed in the alleged the strike.
Syrian Observatory for Human Rights reported that "loud explosions" were heard in the Misyaf area.
According to Syrian reports four Israeli fighter jets took part in the attack, with three missiles being intercepted by Syria's airspace defense system.
Last September, both Syrian and Lebanese media reported that a strike had taken place near the Syrian Scientific Studies and Research Center (CERS), with some of its S-60 missiles being transferred to Hezbollah.
CERS weapons program includes the development of the S-60 in preparation for transfer to the Shi'ite terror organization. The center relies on scientific knowledge provided by North Korea and Iran.
Last week, Syrian state media said Israeli rockets had struck a Syrian military position near Nairab airport on the outskirts of the city of Aleppo.
Israel, concerned that Iran's growing presence in Syria poses a threat to its security, has escalated in recent months its strikes on suspected Iranian and Iran-backed positions in Syria.
Iran is a key ally of Syrian President Bashar Assad and supports a number of militias, including Lebanon's Hezbollah, who have thousands of fighters joining battles in support of his rule.
The reports come merely hours after the IDF completed overnight Saturday an operation to rescue 422 Syrian civil defense activists, along with their families, from a war zone area in southern Syria, the German newspaper Bild reported on Sunday.
It was the first such Israeli intervention in Syria's lengthy civil war, now in its eight year.
According to the report, the rescued activists belong to the White Helmets, officially known as Syria Civil Defence, which is a volunteer organization that operates in parts of rebel-controlled segments of the country and which works to rescue and assist civilians caught in war zones.
Reuters contributed to this article.