The violence in Syria's coastal region marks the biggest test for interim President Ahmed al-Sharaa since he seized power in December, with hundreds of civilians reportedly killed in Alawite villages as government forces sought to crush the insurrection by members of Assad's minority Alawite sect.
Sharaa, an al-Qaeda leader before cutting ties to the group in 2016, has accused remnants of the Assad regime of seeking to drag Syria back into civil war.
He has also announced the establishment of a fact-finding committee into the violence and vowed to hold to account those involved in civilian bloodshed.
In a Reuters interview, Sharaa said mass killings of Alawites were a threat to his mission to unite Syria and promised to punish those responsible, including his own allies if necessary.
The violence has shaken his grip as his administration grapples with myriad challenges, notably getting US sanctions lifted and winning international backing for his efforts to stitch Syria back together after 14 years of conflict.
Germany said reports of the killing of civilians and prisoners were shocking, a day after US Secretary of State Marco Rubio condemned "the radical Islamist terrorists, including foreign jihadis, that murdered people in western Syria".
A spokesperson for the German foreign ministry said on Monday the transitional government had a responsibility to prevent further attacks, to investigate the incidents and to hold those responsible to account.
"We urgently call upon all sides to put an end to the violence," the spokesperson said.
Violence spiralled on Thursday, when the authorities said their forces in the coastal region faced a well-organised attack by fighters aligned with the ousted Assad government.
As government reinforcements deployed, mosques in regions loyal to the new administration began calling on people to wage jihad, or holy struggle, in support of security forces.
By Friday afternoon, reports began emerging that scores of civilians had been killed in sectarian reprisals in Alawite towns and villages.
As of Sunday evening, the Syrian Observatory for Human Rights, a UK-based organisation that reports on the conflict, said 973 civilians were killed in reprisal attacks carried out by government forces or fighters aligned with them.
More than 250 Alawite fighters were killed and more than 230 members of government security forces were also killed, it said.
Reuters has not been able to independently verify the tolls.
Declaring an end to the government's military operation, defence ministry spokesman Hassan Abdul Ghany said government forces "were able to neutralise" Assad regime remnants in seven locations and that security forces would co-operate with the investigation.
"We are paving the way for life to return to normal and for the consolidation of security and stability," he said in statements published by state media.
Plans were in place to continue combating former regime remnants and eliminate any future threats, he said.
Israeli Foreign Minister Gideon Sa'ar said the violence showed that Syria's new rulers "remained jihadists, even if some of their leaders have put on suits".
"It must draw conclusions from what has happened and explore ways to protect minorities in Syria," he told a political party meeting.
