MANILA — Fighting intensified in the embattled southern Philippine city of Zamboanga on Saturday as hopes for a quick cease-fire with Muslim rebels evaporated amid some of the most serious violence to strike the troubled region in years.

The six-day standoff with the rebels in Zamboanga, one of the most vibrant trading cities in the southern Philippines, was believed to have left at least 55 people dead. It has also raised fears of a setback in the government’s efforts, backed by the United States, to calm insurgencies and fight terrorism.

The government said most of the dead were rebels holed up in several seaside neighborhoods. Government forces were firing mortar rounds into the area and battling street by street to take areas back from the militants.

The situation was serious enough that the country’s top civilian and military leaders traveled to the city, despite the mayhem, to plan their strategy. President Benigno S. Aquino III arrived Friday, with one of his escort helicopters taking small-arms fire as he landed. The crisis has crippled the once peaceful city, a mostly Christian enclave on the island of Mindanao, displacing more than 62,000 people.