His appeal comes a day after his defence minister said foreign intelligence reports showed a leader of the Abu Sayyaf rebel group was getting instructions from Islamic State to expand in the Philippines, in the strongest sign yet of links to the Middle Eastern militants.
Duterte said he could no longer contain the extremist "contamination" and urged two Muslim separatist rebels groups - the Moro Islamic Liberation Front and the Moro National Liberation Front - to rebuff Islamic State's advances.
"I am earnestly asking, I am pleading to the MNLF and the MILF, do not provide sanctuary to the terrorists in your areas," he told troops at a military camp in Mindanao, his home region.
"Because if that happens, then we will be forced to go after them within your territory, and that could mean trouble for all of us. I don't want that to happen.
"The government is going after them, they have done wrong, they killed a lot of innocent people."
The south of the predominately Christian Philippines has for decades been a hotbed of Muslim insurgency but Duterte is worried some smaller groups and splinter factions that have pledged allegiance to Islamic State could host IS fighters being driven out of Iraq and Syria.
They include the Maute group in Lanao del Sur province and the Abu Sayyaf in the Sulu Archipelago near Malaysia.
Abu Sayyaf, which means "bearer of the sword", is notorious for piracy and kidnapping and for beheading foreign hostages for whom ransoms are not paid.
It has used the Islamic State flag in hostage videos posted online.
Duterte said he could no longer contain the extremist ,contamination, and urged two Muslim separatist rebels groups to rebuff Islamic State's advances.
Philippine President Rodrigo Duterte on Friday pleaded with the country's Muslim separatist groups to deny sanctuary to militants with links to Islamic State, warning a war would ensue that would put civilians in danger.
