The Israeli military, which has carried out hundreds of strikes in Syria since its civil war started in 2011, had told AFP "we do not comment on reports in the foreign media" when asked about the operation that began late Sunday.
Syrian authorities said 18 people were killed in Israeli strikes on "military sites" in Hama province's Masyaf area, while the Syrian Observatory for Human Rights war monitor reported 27 dead.
The Britain-based Observatory said the Israeli forces' assault targeted the Hair Abbas site, a precision missiles production and development factory created and supervised by Iran's Revolutionary Guards.
"Helicopters dropped down dozens of Israeli forces who were able to enter the weapons production site and destroy it," Observatory chief Rami Abdel Rahman told AFP on Friday.
Before troops descended, Israel launched intense strikes that also destroyed a separate "scientific research centre" in Masyaf used for weapons development where Iranian experts worked, he added.
Israeli warplanes and drones were involved in the operation, which took more than three hours, said the Observatory, which relies on a network of sources inside Syria.
Syria has sought to stay out of the Israel-Hamas conflict, which began with the Palestinian militant group's October 7 attack on Israel.
But strikes blamed on or claimed by Israel have hit Syria frequently since then, including targeting Lebanon's Hezbollah, which has traded near daily fire with Israeli forces in support of ally Hamas.
US news site Axios, citing three sources briefed on the operation, reported Thursday that an Israeli army elite unit "destroyed an underground precision missile factory that Israel and the US claim was built by Iran".
The factory's destruction "appears to be a significant blow to an effort by Iran and Hezbollah to produce precision medium-range missiles on Syrian soil", the report said.
Iran "decided to build an underground factory deep inside a mountain in Masyaf because it would be impenetrable to Israeli air strikes", it added.
The New York Times reported that an Israeli "commando raid" in Syria "obliterated a Hezbollah missile production facility near the Lebanese border", citing American and other Western officials.
"The operation included a daring raid by Israeli special forces, who rappelled down from helicopters and apparently seized materials from the missile facility," according to the report.
Syria and Iran had blamed Israel and condemned the raid, with Tehran calling it a "criminal attack".
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