JERUSALEM — Israeli warplanes struck several military sites in Syria overnight and killed several fighters and civilians, Syrian state media reported on Monday, in what appeared to be a stepping up of Israel’s long-running, partly covert campaign to thwart Iranian military entrenchment in Syria and stop weapon transfers to Lebanon.

The warplanes fired missiles from Lebanese airspace, according to SANA, the official Syrian news agency, which reported that a baby was among four civilians who were killed. The airstrikes hit a variety of targets, according to the Syrian Observatory for Human Rights, a British-based monitoring group identified with the Syrian opposition.

The targets included the headquarters of the Islamic Revolutionary Guards Corps of Iran in the south of the Syrian capital, Damascus; a scientific research center in the countryside around the city; and positions held by Hezbollah, the Iranian-backed Lebanese group, in the mountains near the border with Lebanon, the Observatory said.

The Hezbollah sites that were targeted included ammunition warehouses, resulting in explosions and huge fires, the Observatory reported.

Israel has carried out many strikes in Syria. The military and government officials declined to comment, in line with their usual policy of ambiguity, an approach intended to avoid forcing the government of Bashar al-Assad or his allies into retaliating.

The attack came amid escalating tensions in the region between Iran and the United States over sanctions and the downing of an American reconnaissance drone, and just hours before the International Atomic Energy Agency reported that Iran had surpassed a key limitation on how much nuclear fuel it can possess.

Last week, Israel hosted an extraordinary meeting of the national security advisers of Israel, Russia and the United States that was planned long before the recent rise in tensions. Iran and Hezbollah, both archenemies of Israel, together with Russia, have helped Mr. Assad of Syria gain the upper hand in a civil war that began in 2011.

Opening that trilateral meeting in Jerusalem, Prime Minister Benjamin Netanyahu of Israel pressed for the withdrawal of all foreign forces from Syria, in particular those of Iran and Iranian proxies near the frontier with Israel. He said Israel had acted “hundreds of times” to prevent Iranian military entrenchment in Syria and the transfer of weapons.

The Israeli campaign, however surgical, risks miscalculations and unintended consequences. Last year, Syrian forces accidentally shot down a Russian military plane after an Israeli airstrike on Syrian territory, causing a temporary crisis in Israeli-Russian relations.

On Monday, the foreign minister of Turkish-held Northern Cyprus, Kudret Ozersay, said that what appeared to be a Russian-made antiaircraft missile fired by Syria at Israeli jets had missed its mark and fallen on the island. There were no reports of casualties.

Citing a military source, the Syrian news agency, SANA, said that Syria’s air defense had responded to the missiles fired by Israeli warplanes.

Another figure close to the Syrian government who was briefed on the strikes and who requested anonymity to discuss secret military information put the total death toll from the attacks higher, saying that at least 16 had been killed, including five Syrian Army personnel, one Iranian and 10 civilians and that 49 others had been wounded. He added that many of the targets had been vacated ahead of time because of the tensions between Iran and the United States and that the civilian casualties had been caused by explosions from munition stores.

Though hardly a supporter of Mr. Assad, Israel has professed neutrality in the Syrian civil war, saying that it only acts in the country in the interests of maintaining its own red lines and protecting its own interests. Israel has said it would like to see stability restored there.

Speaking on Monday at an annual conference on national security, Yossi Cohen, director of the Mossad, Israel’s intelligence service, said that the country had “no interest in a conflict with Syria, but we cannot agree to Syria serving as an arena in which Iranian forces or forces operated by it become entrenched against us.”

Without specifically addressing the overnight activity, Mr. Cohen added that Israel would not allow Syria to become a logistical base for the transfer of weapons to Hezbollah and Lebanon.

“Israel has operated in the past four years, overtly and covertly — only a small part of that has been reported — to prevent and destroy the entrenchment of Iranian forces in Syria and the infrastructure for manufacturing precision weapons,” he said. “Thanks to that resolute action, I believe the Iranians will ultimately reach the conclusion that it’s not worth their while.”

He said that Iran and Hezbollah were now seeking to move some of their bases to northern Syria, “a place where they believe, mistakenly, that we will have trouble reaching.”

Follow Isabel Kershner on Twitter: @IKershner.

Hwaida Saad contributed reporting from Beirut, Lebanon; and David M. Halbfinger from Herzliya, Israel.

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