Israeli warplanes struck Syrian military headquarters and near the presidential palace in Damascus on Wednesday, as sectarian clashes in the southern part of the country quickly spiraled into a crisis for Syria’s new government.

Israel said it intervened to stop government attacks on the Druze, a religious minority community that spans the border between the two countries, carrying out a wave of airstrikes on Syrian government tanks and military convoys maneuvering in the south.

The violence began with recent clashes between local Druze and Bedouin populations around the town of Sweida in southern Syria. Community leaders, activists and Israel’s military said the violence worsened after government forces intervened.

On Wednesday, Druze residents of Sweida reached by phone described scenes of executions, house burnings and looting. Several thousand residents fled toward the Jordanian border to escape the violence, while thousands more fled into the countryside.

“Yesterday a rocket hit my building while I was inside,” said Wajiha Hajjar, a lawyer and activist who was trying to cross into Jordan on Wednesday. “Thank God we survived.”

Druze in Israel surged across their border to protect relatives. Israeli Prime Minister Benjamin Netanyahu said the military was working to defend their fellow Druze and urged them not to cross into Syria.

“Do not cross the border,” he said. “You are endangering your lives.”

Israel’s military said that it was reinforcing the border and deploying more troops for potential operations.

Since Monday, around 150 people have been killed and some 300 injured, according to Ayman Shib Al Deen, a Druze lawyer and activist who tracks the number of violent deaths by visiting hospital morgues.

Some community leaders and activists in Sweida accused government forces and allied militias of targeting Druze. Late Wednesday, the office of Syrian interim President Ahmed al-Sharaa said it was aware of violations committed in Sweida and said any entity acting outside the law would be held accountable.

Syria’s fledgling government denounced Israel’s latest attacks as a violation of its sovereignty. The country’s military said 18 troops had died in the clashes, while its health ministry said three people were killed and 34 injured in the strikes in Damascus.

“We are very worried about the violence in southern Syria,” U.S. Secretary of State Marco Rubio said. “It is a direct threat to efforts to help build a peaceful and stable Syria.”

He characterized the clashes between Israel and Syria as a misunderstanding and said the U.S. was working to de-escalate the situation.

Members of Syria’s Druze community amid clashes.

A member of the Syrian security forces during clashes in Sweida, Syria.

After the collapse of the Assad regime late last year, Israel carried out a wave of attacks that wiped out the former government’s military and sent troops in to seize strategic positions in southern Syria, saying it aimed to protect its security and prevent cross-border attacks on its citizens.

The longtime foes had more recently been in talks to set aside hostilities, and Israel’s foreign minister expressed hopes last month that they could establish diplomatic relations. But they are now plunging deeper into a conflict that presents one of the most serious challenges so far for the collection of former jihadist rebels who toppled the Assad regime.

“It is a significant escalation overall,” Nanar Hawach, senior analyst for Syria with the International Crisis Group, said of the recent fighting. “In addition to Israel intervening, it also highlights the fragility of the situation in Syria and how intercommunal tensions could quickly spiral into an international kind of conflict where the Ministry of Defense has been bombed. It is significant on various levels.”

The small Druze minority in Israel plays an outsize role in Israel’s security. They are loyal to the state and have fought in Israel’s military since the founding of the country. When their communities in other countries are attacked, they expect Israel to intervene, said Eman Safady, an Israeli Druze journalist and expert on Middle East politics.

“The Druze fought alongside the Jews on Oct. 7, and we lost many of our own,” Safady said, referring to Hamas’s deadly invasion of Israel in late 2023 that sparked the war in Gaza. “The expectation now is that Israel and the Trump administration will stop these massacres.”

The Syrian Defense Ministry building in Damascus.

Israel has its own security interests in southern Syria and hopes to use an alliance with the country’s Druze to help keep possible enemies away from the border. But Syria’s Druze are divided over Israel’s involvement in their country. Some who don’t support Israeli involvement fear being branded as collaborators, while others say it keeps Syria weak.

The fighting between Sunni Muslim Bedouin tribes and Druze militias in Sweida, 57 miles south of Damascus, followed the kidnapping and robbery of a Druze vegetable merchant.

The violence snowballed into armed confrontations between the Bedouin and Druze, whose religion is rooted in an ancient offshoot of Shiite Islam. Clashes spread across the province, prompting Syrian government forces to intervene.

In early May, in another part of southern Syria, an audio recording purporting to feature a Druze criticizing the Prophet Muhammad swiftly escalated into sectarian violence, leaving a number of dead, including civilians and 16 members of state security forces.

Syria’s government has been widely criticized by many Druze and other minorities for not being inclusive enough and for lending support or looking the other way as armed groups target minorities. In March, hundreds of Alawites—a religious minority to which the Assad family belongs—were killed by militias and foreign fighters loosely aligned with the government.

The Syrian government has repeatedly said it represents all citizens.

On Wednesday, the government and some Druze groups in Sweida announced a cease-fire, the second in as many days.

Corrections & AmplificationsAhmed al-Sharaa is the president of Syria. An earlier version of this article misspelled his last name as al-Shaara. (Corrected on July 16)