Three days of clashes between fighters affiliated with Syria’s new leaders and those loyal to the ousted dictator Bashar al-Assad have left scores of civilians dead, according to two war monitoring groups, who reported on Saturday that many of them had been killed by the government’s forces.

The British-based Syrian Observatory for Human Rights, which has monitored the Syrian conflict since 2011, said early Sunday that more than 1,000 people had been killed in the coastal provinces of Tartus and Latakia. That figure included about 700 civilians, most killed by government forces. The information could not be independently verified.

Another monitoring group, the Syrian Network for Human Rights, reported earlier that government security forces had killed some 125 civilians. It said that men of all ages were among the casualties and that the forces did not distinguish between civilians and combatants.

Information Ministry officials, responding to the charges of killing civilians, said they rejected “undocumented allegations accusing government forces of committing violations.” But they also said the government was committed to conducting comprehensive investigations and would hold to account those found to have harmed civilians.

“The Syrian government confirms that its forces operate according to strict standards that respect international humanitarian law and are keen to protect civilians during their operations,” a ministry statement said.

The Observatory said most of the civilians killed were from the country’s Alawite religious minority, to which Mr. al-Assad belongs, but this could not be independently verified either. The monitoring group said scores of combatants on both sides of the conflict had also been killed.

The Syrian Network for Human Rights said the Assad loyalists had killed more than 100 security forces for the new government.

The Defense Ministry told Syrian state media on Saturday afternoon that forces had regained control over most areas that had been taken by the former regime remnants ,and that roads leading to the coastal area had been closed “to regulate violations, prevent transgressions and gradually restore stability to the area.”

The unrest has been the bloodiest outbreak of violence since the Assad regime was ousted in early December by rebels who became the country’s new leaders. It presents a major test of the new government’s authority and has raised the specter of a larger sectarian conflict in Syria, where tensions were already high as a result of the civil war.

By Saturday afternoon, the Syrian Red Crescent had been given permission to enter one of the towns to evacuate the injured, said Haidera Younes, a spokesman for the Red Crescent’s branch in Tartus.

The clashes began on Thursday after Assad loyalists killed 16 government security personnel in Latakia province, in the deadliest attack yet on Syria’s new security forces, according to government officials and the Observatory.

Violence quickly spread across Latakia and Tartus provinces, longtime strongholds of Mr. al-Assad along the Mediterranean coast and home to most of the country’s Alawites. Armed remnants of the ousted regime are believed to be scattered across the two provinces and have presented a challenge to the country’s new leaders as they try to exert their authority and unite a fractured country after more than 13 years of civil war.

The government responded to the initial attack on Thursday by deploying thousands of security forces and soldiers from other parts of the country to the restive coast. The government has sought to present the clashes as a legitimate authority fighting the remnants of a brutal regime.

For the first time, the new government forces deployed helicopters outfitted with machine guns on Thursday around the mountainside of the coastal region, according to a government official on the coast, who asked not to be named because he was not authorized to speak to reporters. The helicopters were deployed to areas where armed Assad loyalists were stationed, the official added.

A video verified by The New York Times and filmed along the coast west of Latakia airport appears to show government fighters repurposing Russian-made anti-submarine depth charges by dropping them as bombs from the rear of a helicopter. A spokesman for the government in Latakia did not respond to a request for comment about the video. A journalist with Syrian state media, Muhammad al-Othman, said that the munitions were dropped over mountainous areas where old regime remnants remain.

The Assad regime drew international condemnation for its frequent use of helicopters for indiscriminate bombings, dropping improvised “barrel bombs” onto civilian populations for years. The use of anti-submarine munitions for that purpose fits the old regime’s pattern of using whatever it could either fabricate or repurpose for launching aerial attacks via helicopter.

The munitions used in the helicopter attacks appeared to be Russian RBG-25 depth charges, which are normally launched from ships for use against submarines, said Trevor Ball, a former U.S. Army explosive ordnance disposal technician. They most likely originated from old Assad regime stocks, he said.

“This is quite a bit different from how they are designed to be deployed,” said Mr. Ball. “These aren’t going to cause as much damage as the barrel bombs the Assad regime commonly used.”

Christina Goldbaum, Muhammad Haj Kadour and Reham Mourshed contributed reporting.