President Rodrigo Duterte on Thursday said he would ask the leaders of Indonesia and Malaysia to "blast" pirates out of regional waters and would refocus security efforts to solve the problem.

The Abu Sayyaf, a kidnap-for-ransom network that has pledged allegiance to the Islamic State group, has been kidnapping dozens of sailors on fishing vessels and cargo barges, prompting warnings the region could become the "next Somalia."

Duterte's remarks came two days after he declared the southern city of Marawi "liberated from terrorists' influence" following a nearly five-month battle against militants including Abu Sayyaf members.

"Blast them out of the seas to keep our shipping lanes open and safe. They have committed enough piracy there, enough money collected from ransoms," Duterte said in a speech at a forum for Southeast Asian diplomats and leaders in Manila.

"I just finished the war in (Marawi) then perhaps I can refocus the entire Armed Forces to deal with this problem once and for all."

Pro-IS gunmen occupied parts of Marawi on May 23 in what Duterte said was a bid to establish a Southeast Asian caliphate there.

The country's longest urban conflict has claimed more than 1,000 lives and displaced 400,000.

While declaring that the fighting in Marawi was winding down, Duterte on Thursday said Islamist militants continued to threaten Southeast Asia's supply routes and shipping lanes.

He specified the Malacca Strait, one of the world's busiest shipping lanes between the Malaysian peninsula and Indonesia's Sumatra island, as suffering from "terrorism."

"Something has (to be done), a drastic action for a very dangerous situation," Duterte said.

The threat from Islamist militants will be on the agenda in a meeting of Southeast Asian leaders and their allies next month as well as in a gathering of the region's defence ministers next week.

The Philippines, Malaysia and Indonesia have launched coordinated air and sea patrols to combat the security threat.