It also hit a military base nearby where ground-to-ground missiles were kept, the group said.

A BBC report in May named the Masyaf site as one of three places where the agency produced chemical weapons.

Andrew J. Tabler, a Syria expert and fellow at the Washington Institute for Near East Policy, said the United Nations confirmation that Syrian forces had used sarin gas in the April attack would draw attention to the research agency because it would have produced the gas.

But at least as worrying for Israel and other regional powers, he said, was the military base near the Maysaf site that was reported to be producing advanced weapons, particularly missiles capable of carrying chemical weapons. That base was frequented by Iranian forces in Syria who are supporting Mr. Assad’s military, raising fears that weapons made there could be passed to Hezbollah, the Iranian-backed Lebanese militia, or to other Iranian-backed militias.

“The larger context is that the Iranians are in the driver’s seat in Syria,” Mr. Tabler said. “They are playing an unprecedented role.”

Israel has repeatedly hit targets in Syria during the country’s six-year civil war, most of them thought to be armament warehouses or convoys carrying weapons to Hezbollah.

Yaakov Amidror, a former Israeli national security adviser, said the strike on Thursday went a step further. “The big change now is that somebody decided to go to another level of hitting: to the producing stage,” he said in an interview.

As is common with strikes in Syria, Israeli officials declined to comment on it. But Defense Minister Avigdor Lieberman, while insisting that Israel was not seeking “any military adventure in Syria,” said in a radio interview on Thursday that Israel was determined to resist Iran’s influence in the region.