MANILA — Sporadic fighting continued Sunday in Zamboanga City, the embattled southern Philippine city where government officials a day earlier had declared an end to a three-week standoff with separatist militants.

Six rebels were killed in fighting while bomb-sniffing dogs hunted down unexploded ordnance and hidden explosive devices, officials said Sunday. An undetermined number of rebels continued to fight in the obliterated neighborhoods where the fiercest battles had taken place.

More than 200 people — rebels, soldiers, police officers and civilians — have been killed during the standoff, which began Sept. 9 when several hundred members of the Moro National Liberation Front entered the city to raise their flag and declare independence.

After the rebels were confronted by troops, they took more than 100 hostages and battled soldiers in five seaside neighborhoods of the city. Soldiers fought house to house to regain control of the rebel-held areas, and senior officials said in recent days that the conflict was winding down.