Isnilon Hapilon's death came during a push to end the four-month siege of Marawi, a battle that has claimed more than 1,000 lives and raised fears that IS was seeking to set up a regional base in the southern Philippines.
Security analysts say Hapilon has been a key figure in the jihadist outfit's drive to establish a caliphate as they suffer battlefield defeats in Iraq and Syria.
"Their bodies have been recovered by our operating units."
The US government had offered a USD 5 million bounty for information leading to Hapilon's arrest, describing the 51- year-old as a senior leader of the southern Philippines-based Abu Sayyaf group, which the US considers a "foreign terrorist organisation".
Lorenzana said Philippine ground forces mounting a final assault on the militants in Marawi killed Hapilon and Omarkhayam Maute, one of two brothers who lead a militant group allied to Hapilon, early today.
"The implication of this development is that the Marawi incident is almost over and we may announce the termination of hostilities in a couple of days," Lorenzana said.
Philippine authorities have made several previous announcements on the imminent end of the conflict, but observers believe this time the forecast is likely to be accurate.
Pro-IS gunmen occupied parts of Marawi, the Islamic capital of the mainly Catholic Philippines, on May 23 following a foiled attempt by security forces to arrest Hapilon, authorities said.
Since then more than 1,000 people have been killed and 400,000 residents displaced.
Defence chiefs last month said other Philippine militant leaders had been killed in the battle for Marawi.
Troops were still pursuing Malaysian militant leader Mahmud Ahmad in the Marawi battle zone, Lorenzana said.
The insurgents have withstood a relentless US-backed bombing campaign and intense ground battles with troops that have left large parts of Marawi in ruins.
Troops identified Hapilon and Maute's location yesterday based on information from a hostage who had escaped, Lorenzana said.
"We will put our efforts and energies on the challenging task of rebuilding and rehabilitating Marawi," presidential spokesman Ernesto Abella said.
Hapilon is believed to have been involved in 2001 kidnappings of three Americans, two of whom were later killed.
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