The patrols will be conducted by forces from Indonesia, the Philippines and Malaysia, starting with sea operations from June, with air and land patrols starting at a later date.
The initiative in the Sulu Sea, an area bounded by the Malaysian state of Sabah and the southern Philippines, is a "collective agreement that is followed by the operational level," Indonesian Defense Minister Ryamizard Ryacudu said. It will feature joint command posts and exercises between the trio's ground forces.
Indonesia has the world's largest Muslim population. Ryamizard was speaking at the Shangri-La Dialogue, a security conference in Singapore attended by defense ministers and experts from 39 countries.
The presence of Islamic militants has been felt the region. Philippine troops are struggling to end a bloody siege by 500 Islamic State group-aligned extremists in the southern city of Marawi, one of the boldest militant attacks in Southeast Asia in years.
The joint patrols are not conducted under the umbrella of the 10-member Association of Southeast Asian Nations, of which Indonesia, the Philippines and Malaysia are part.
"ASEAN is not a military bloc. It is a defense corporation. If there are any issues, we have to find commonalities" out of the organisation, Ryamizard said. Still, the objectives are aligned.
Singapore Defense Minister Ng Eng Hen said that he has offered assistance, in the form of an information-sharing center at Changi Naval Base.
China has been asked to contribute its ships. Responding to a question from a member of the Chinese delegation, Ryamizard said: "It is like peace patrols. It is very important to underline that it is joint peace patrols."
The inclusion of China is sensitive as the country has pitted itself against smaller Southeast Asian neighbors in claiming disputed islands, coral reefs and lagoons in the South China Sea.
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