MANILA — The Philippine military said on Sunday that troops had found the bodies of 16 people believed to have been killed by Islamic militants, as fighting continued for a sixth day for control of Marawi City in the southern part of the country.
The discovery of the bodies underlined the civilian toll from the siege, with tens of thousands of residents fleeing the city and the military using aerial bombing and ground troops in an effort to drive the militants from their strongholds.
On Tuesday, President Rodrigo Duterte declared a 60-day period of martial law in the south to expand his authority to fight the militants. Late Friday, he expressed support for the troops by joking that they could each rape three women without suffering any consequences. His comment sparked outrage around the world.
The authorities put the death toll from the six days of fighting at 95, including 61 militants, 19 civilians and 15 soldiers and police officers.
The fighting began on Tuesday, after government forces attacked a group of militants said to be protecting Isnilon Hapilon, the leader of Abu Sayyaf, an Islamist gang that kidnaps people for ransom. Mr. Hapilon has been designated by the Islamic State group as its leader in the Philippines. The United States has offered a $5 million reward for his capture.
The military has said that Mr. Hapilon was sighted in Marawi, a city of about 200,000 people on the southern island of Mindanao, and that he is believed to be in the area still.
It is unclear why Mr. Hapilon would have ventured there from his relatively secure jungle base, thought to be on the remote island of Basilan, about 300 miles away.
The military previously said that Mr. Hapilon had been injured in a January bomb strike and that he had suffered a mild stroke, which would call into question his fitness for a journey to Marawi City over rugged terrain.
Whether he is in the city or not, the military apparently underestimated the strength of the militants there, mainly members of the Maute organization, a group affiliated with Abu Sayyaf that also embraces the Islamic State. The military also said that foreign militants from Indonesia, Malaysia and Singapore were among those taking part in the clashes.
The Maute fighters quickly took over much of the city, torching a cathedral and a hospital, among other buildings, and posting snipers to keep government troops at bay.
“Precision airstrikes and artillery fire will likewise continue at specific targets to hasten the clearing,” said Brig. Gen. Restituto Padilla, a military spokesman.
General Padilla said that the 16 civilians’ bodies had been found in two locations. One group of eight was found near Mindanao State University and included four men, three women and a child, he said.
The bodies of the eight other victims were found in a ditch at the edge of the city with their hands tied and gunshot wounds to the head, the television station ABS-CBN reported. Near their bodies was a cardboard sign that said, “Munafik,” which can mean hypocrite or traitor.
Residents in the area said the eight were men who had worked at a bakery and had been attempting to join the stream of refugees heading north to nearby Iligan City when they were stopped by Maute gunmen.
“This development validates a series of reports of atrocities committed by the militants earlier,” General Padilla said.
The authorities and relief workers said that more than 30,000 people from Marawi City had taken refuge in evacuation centers and that more than 42,000 had fled to relatives’ homes outside the city.
Mr. Duterte, during a visit with troops on Friday in Iligan City, told the soldiers to do their jobs under martial law and he would take responsibility for the consequences.
“For this martial law and the consequences of martial law and the ramifications of martial law, I and I alone would be responsible; just do your jobs,” he said. “I will go to jail for you. If you raped three, I will own up to it.”
Mr. Duterte said he drew the line at taking “a fourth wife,” as the crowd laughed.
The comment was reminiscent of his statement during the election campaign last year that he should have been the first to rape an Australian missionary who had been taken hostage by prison inmates and killed.
It also echoed his remarks that he would support police officers involved in his violent campaign against drugs. The police and vigilantes have killed more than 4,000 in the antidrug campaign since Mr. Duterte took office 11 months ago.
The latest comment prompted a storm of protest on social media. Chelsea Clinton said on Twitter: “Duterte is a murderous thug with no regard for human rights. It’s important to keep pointing that out & that rape is never a joke.”
Others criticized President Trump for praising Mr. Duterte’s handling of the antidrug campaign during a recent phone call.
“President Duterte is a grotesque man,” tweeted Preet Bharara, the former United States attorney in Manhattan who was fired by Mr. Trump this year. “Maybe our president will stop needlessly patting him on the back.”
Ernesto Abella, Mr. Duterte’s spokesman, defended the president’s latest comment, saying that Mr. Duterte was attempting to show his support for the soldiers.
“In Iligan, he gave his full support to the men and women in uniform, taking complete responsibility for their actions, even exaggeratedly describing crimes like taking a fourth wife,” Mr. Abella said.
But Etta Rosales, who was arrested, tortured and raped under martial law during the rule of Ferdinand Marcos, said Mr. Duterte’s words reveal his misogynist and authoritarian character.
“He appears to exhibit the mind-set of a criminal, a woman hater, a person who thrills and derives dark pleasure from attacking treasured norms and values of families and societies,” she said. “Thus he has no tolerance for human rights, which stand in the way of authoritarianism.”