Murad Ebrahim has billed his Moro Islamic Liberation Front (MILF), which has made peace with the government, as a rival to IS for the hearts and minds of angry young Muslims in the impoverished south of the mainly Catholic nation.

Murad said the MILF was battling pro-IS groups for influence in schools as the jihadists worked to infiltrate madrasas (Islamic religious schools) and secular universities.

At the same time IS gunmen were making their way into the southern Philippines from Malaysia and Indonesia, he added, but gave no estimates.

A five-month siege flattened the city of Marawi on the southern island of Mindanao, the Philippines' main Islamic centre, and claimed more than 1,100 lives.

Murad told reporters conditions on the ground were still ripe for another Marawi-style siege.

"This ISIS group continues to penetrate us because they are being displaced in the Middle East and they want to have another place," Murad said, using an another name for IS.

"The chances of having another Marawi cannot be overruled."

The Marawi attackers found and looted stockpiles of munitions, cash and jewellery from homes -- some owned by MILF members -- before the city was retaken by US-backed Filipino troops in October, he said.

"When they (MILF members) fled from Marawi they (could) not bring their vaults. That is where the ISIS was also able to get so much money and now they're using it for recruitment," he added.

"It's very sad. In our country some people say buying weapons and ammunition is just like buying fish in the market."

The combination of weak central government authority, the presence of rebel groups and long-running blood feuds means Mindanao is awash with weapons, he added.

Manila signed a peace deal with the 10,000-member MILF in 2014 after decades of Muslim rebellion in Mindanao for independence or self-rule that had claimed more than 100,000 lives.

Murad urged President Rodrigo Duterte's government to speed up the passage of a Muslim self-rule law to flesh out the peace accord, warning pro-IS militants were recruiting for a new attack.

"If the (self-rule law) will not be passed now I think it will develop a situation where these extremist groups can recruit more adherents, because it will prove their theory that there is no hope in the peace process," he said.

"Since they have the capability also to supply money and then they also have the ability to make explosives, bombs, they can just use these young recruits to work out their plan."