Ground troops hid behind walls and armored vehicles and exchanged volleys of gunfire with Maute group fighters, shooting into elevated positions occupied by militants who have held Marawi City on Mindanao island for two days. Army tanks packed with soldiers rolled into the southern Phili.
Police Chief Romeo Enriquez said there may have been confusion because his predecessor in Malabang, a town near Marawi, was killed in the fighting on Tuesday, although he was not beheaded.
At least 46 people - 15 security forces and 31 rebels - have been killed and religious leaders say militants were using Christians taken hostage during the fighting as human shields. The violence sent thousands of people fleeing and raised fears of extremists gaining traction in the country.
De Borja says many civilians were evacuated, and the areas are being secured.
Authorities have not reported any civilian casualties but the GMA television network showed images of nine people who had apparently been shot dead. Military chief of staff Gen. Eduardo Ano said the militants erected Islamic State flags at several locations.
As authorities worked to clear the city, residents spoke of their terror. "I'm just praying that the bullets will not find their way to my house and hit us".
"I hope they free them, including Fr. Chito and my wife and their companions, because they are innocent", he told Manila's DZMM radio. Marawi has a population of around 200,000.
Duterte - who has been waging a controversial war on drugs that has incited violent vigilantism and claimed thousands of live - said he would consider expanding martial law across the entire country if the threat continued.
Hapilon, an Arabic-speaking Islamic preacher known for his expertise in commando assaults, is a commander of the Abu Sayyaf militant group.
"Based on our intelligence, Isnilon Hapilon is still in the city", Herrera said.
"According to the Filipino government, militants belonging to the Maute Group and the Abu Sayyaf Group - two local groups that have pledged support to so-called Islamic State (IS) - swarmed the streets of Marawi on Tuesday", the BBC explained. "The situation is under control, meaning they know exactly where the members of this terrorist group are located", he said.
Meanwhile, The Straits Times quoted Philippines military spokesman Brigadier-General Restituto Padilla as saying that Singaporeans were also involved in the fighting in Marawi.
He added that, "By imposing martial law against Maute and other rebel groups, Duterte practically closes his eyes to the reality that popular armed resistance in our society, whether by various Moro revolutionary fronts or the New People's Army, is rooted in long-standing economic, social, and political injustice".
The United States regards Hapilon as one of the world's most unsafe terrorists, offering a bounty of $5 million for his capture. He was wounded in a Philippine airstrike in January but got away.
The siege started Tuesday after government troops attempted to raid a hideout of a top militant. Once again, Hapilon escaped.
Earlier, the Western Mindanao Command said the number of government forces killed in the ongoing clashes between government forces and Maute fighters in Marawi City had risen to seven.
Much of Marawi, which is in Lanao del Sur province, was still a no-go zone Thursday. Plumes of black smoke rose from the direction of the city center and air force helicopters swooped overhead.
Checkpoints were established at entry and exit points of Marawi City, while helicopters hovered over the city and more soldiers arrived in trucks to secure the municipality. The Philippines is Asia's largest Roman Catholic nation, but its southern region has a large Muslim minority.