He also said that he was determined to keep the Islamic State group out of Philippines.
Duterte’s latest remarks on the crisis in Marawi City are a change in stance, when he urged Maute militants to talk with him.
“I will not talk to the terrorists,” he said in a speech to the military in Davao City.
Duterte was outraged by what he believed is insincerity towards a peace process he has started with communist rebels fighting a separate, long-running conflict.
He said the rebels leadership would be arrested if they came back to the Philippines.
The president has previously invited them to return home and even offered them government posts.
In another development, the military said a week-long assault by Islamist rebels in a southern Philippine city is being fuelled with stolen weapons and ammunition and fighters broken out of jails.
The military said the pro-Islamic State Maute group has proven to be a fierce enemy, clinging on to the heart of Marawi City through days of air strikes.
The military deployed for the first time SF-260 close air support planes to back attack helicopters and ground troops looking to box rebels into a downtown area.
The army said the rebels hold about a tenth of the city.
The militants had freed jailed comrades to join the battle and opted to engage in urban warfare because the city had stocks of arms and ample supplies of food.
“Yes indeed, there was planning involved,” Padilla said.
Duterte is alarmed by the strength of the Maute and intelligence reports suggesting it has teamed up with other extremist groups and has recruited foreign fighters.
“I specifically warned everybody there is more dark cloud ahead of us. I was referring specifically to the contamination of ISIS slowly creeping towards our shores,” Duterte told navy personnel in Davao City.
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