The minister explained that a female hostage who escaped the militants' captivity helped locate Hapilon and Maute in one of the buildings in the main battle area in Marawi city.
Troops were still pursuing dozens of fighters in the battle zone including Indonesians and Malaysians, Ano said, after rescuing 20 hostages over the weekend with a two-month-old baby among them.
Rumors of Hapilon and Maute's death have periodically circulated in the past but on Monday Philippine Defense Secretary Delfin Lorenzana confirmed the latest reports to the Philippine Daily Inquirer.
"They were able to get Isnilon Hapilon and Omar Maute".
Hapilon, who is listed as one of the FBI's most-wanted terror suspects, and Maute have always been in the crosshairs of the Philippine state.
He said the 4ID is in close coordination with the Armed Forces of the Philippines' Western Mindanao Command for any intelligence update regarding the movement and presence of the remaining insurgents.
Fighting in Marawi City erupted between when government forces tried to arrest Hapilon who was declared as the "emir" of the terror group ISIS in Southeast Asia last May 23.
The military, boosted by the deaths of two key militant leaders in a gunbattle the day before, hopes the current fighting is the final phase of defeating a dwindling band of fighters who are now trapped in an area the army says is about 2 hectares (5 acres).
The last two surviving leaders of a deadly siege in the southern Philippines, including a top Asian terror suspect, were killed Monday in a push by thousands of troops to retake the last pocket of Marawi city still held by pro-Islamic State militants, top security officials said.
"We will announce the termination of hostilities in a couple of days", Lorenzana added, referring to the months' long siege. Hapilon also had a $5m U.S. bounty on his head for carrying out multiple ransom kidnappings and beheadings of U.S. citizens.
On the other hand, Omar Maute and his brother Abdullah founded a group named after them that pledged allegiance to the Daesh following their return to the Philippines from their studies in Egypt where the imbibed the Daesh teachings. More than 1,000 people have been killed, including about 800 militants. He said "the Maute-IS have established very strong defensive positions", adding that the IS fighters were hiding in dugouts and basements of occupied buildings. "Terrorism will take a new form in the post-Marawi period because these terrorist groups linked to ISIS continue to innovate and their actions are evolving", Rommel Banlaoi, chairman of the Philippine Institute for Peace, Violence and Terrorism Research, told AFP.
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