Father Suganob had been a captive in yet another mosque, Bato Mosque, which the military took control of on Saturday.

“As follow-up and clearing operations continue, we expect the enemy to yield more previously occupied positions, but not without a fight,” said the head of the armed forces, Gen. Eduardo Año. “We are ready for that.”

He said the rebels had been denied “their erstwhile command and control hub,” referring to Bato Mosque, and he called the freeing of Father Suganob “an enormous gain.”

As of Saturday, the death toll from the fighting since May stood at 668 militants and 149 soldiers, according to the military. It said 47 civilians had been killed.

The military estimates that 40 to 60 rebels are still fighting. There has been no word of the fate of Isnilon Hapilon, the declared leader of the Islamic State in the Philippines, or of the brothers Omarkhayam and Abdullah Maute, leaders of an allied militant group.

The Marawi crisis has been the biggest security threat Mr. Duterte has faced since he became president last year. He has admitted that the military was caught off-guard by the militants’ brazen attack, which occurred as he was traveling in Russia with top officials, including military and police generals. Mr. Duterte has since placed the entire southern third of the country under martial law as the security forces pursue the militants and their supporters.

On Saturday, Navy commandos patrolled the city’s lakeshore area armed with high-caliber weapons and night-vision goggles, while P-3 Orion spy planes and drones provided by the United States tracked movements on the ground.

Ground troops, meanwhile, moved through streets littered with debris. Upturned vehicles and rows of heavily pockmarked homes lined the streets, where militants had dug in. The Philippine Air Force carried out bombing runs that sent up plumes of black smoke and rattled windows a half-mile away.

Defense Secretary Delfin Lorenzana said the fighting was nearing an end, although he declined to offer a specific time frame. The military has announced three different dates by which it said the fighting would be over, but it has continued nonetheless.

“There’s only a little resistance left,” Mr. Lorenzana said.

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