Hundreds of people have been killed in Syria after clashes between pro-government and pro-Assad forces escalated into sectarian violence, drawing furious condemnation of the country’s new leaders from the US.

Many of those targeted were Alawites, members of a minority sect to which former president Bashar al-Assad belongs and who dominated the top ranks of the former regime’s security forces.

The violence has become the greatest threat to the country’s stability since Assad was ousted in December, with the defence ministry saying clashes were ongoing in parts of the western coast on Sunday morning.

While estimates varied, war monitor the Syrian Observatory for Human Rights reported that more than 1,000 people had been killed as of Sunday, the majority of them civilians. The Financial Times was unable to independently verify the figures.

US secretary of state Marco Rubio said Washington “condemns the radical Islamist terrorists, including foreign jihadis, that murdered people in western Syria” and stood with the country’s minorities.

“Syria’s interim authorities must hold the perpetrators of these massacres against Syria’s minority communities accountable,” Rubio said.

The US designates Interim President Ahmed al-Sharaa’s Islamist group Hayat Tahrir al-Sham, a former al-Qaeda affiliate that toppled Assad, as a terrorist entity.

Sharaa, who renounced his ties to al-Qaeda a decade ago and promised to protect minorities and form an inclusive administration, on Sunday called for calm.

Filmed speaking in a mosque in Damascus, Sharaa said what happened was among the “expected challenges” and called for coexistence. “We can live together in this country, god willing,” Sharaa, who has been engaging with the US and other western governments to seek sanctions relief, said.

The turmoil began on Thursday after armed factions loyal to Assad clashed with government security forces and called for an “uprising” in Latakia, a coastal province and former Assad stronghold.

This escalated into intercommunal violence and sectarian killings as forces loyal to the interim government arrived from outside the coastal area to crush the pro-Assad forces, according to residents and rights groups.

Many of the former rebel factions now responsible for security under the new interim administration, which disbanded Assad’s army, blame Alawites, along with former regime forces, for atrocities that took place during Syria’s more than 13-year civil war.

Alawite residents told the FT they were sheltering in their homes, had relatives and neighbours killed or were fleeing out of fear of further attacks.

Anas Haidar, an Alawite translator from Baniyas, a city south of Latakia, said he learned from his aunt that armed factions had on Friday taken his 69-year-old uncle on to the roof of his apartment building and executed him along with other men living in the building.

“We thought the sounds we were hearing were shooting in the air or celebrations, but no: all these shots were at people,” he said, adding that his uncle had been a longtime opponent of the Assad regime.

On Saturday, as Haidar was preparing to flee, he received a call from another aunt begging him to come help her son, who was bleeding out after being shot on the roof and later died. Haidar left the neighbourhood in the car of a Sunni friend, who sheltered him and other families for the night.

The escalation poses one of the most serious threats so far to the legitimacy of Syria’s transitional government.

It also underscores the scale of the challenge it faces in unifying and ruling the nation, which is home to multiple sects and awash with weapons and armed factions, including unemployed former soldiers from Assad regime forces.

Around the time of the initial attacks, a group calling itself the Military Council for the Liberation of Syria issued a statement vowing to bring down the government. The group is led by a former commander of the Assad army’s brutal Fourth Division, once led by Bashar’s brother Maher.

In the absence of a unified national security force, Sharaa has incorporated a patchwork of armed opposition factions under the umbrella of the defence ministry earlier this year, but co-ordination, training and ideology varies widely.

Mohammad Salah Shalati, a Sunni sheikh from Latakia, said there was widespread frustration over the perceived lack of accountability for those who worked for the former regime.

“We’ve been telling the government, ‘This or that person used to work against us for the regime’. We know who they are, but they ask for proof,” he said. “The new government tells us to be patient. But Sunnis were oppressed for 60 years . . . After March 6, the people no longer want forgiveness — they want to hold everyone accountable.”

Residents of coastal areas who spoke to the FT emphasised the difference between the behaviour of what they called extremist factions and the more disciplined HTS forces, but said it was up to the new authorities to keep all of them in line.

The factions “are not illegal gangs. Technically they are the law, the military”, Haidar said. “These were groups that were supposedly in the meeting with Ahmed al-Sharaa and agreed to be part of the Ministry of Defence.”