In a speech to lawmakers from the Asia-Pacific region, Yudyuhono warned that the campaign against militants would be a long one, and said it would need to be fought on "political, economical, legal, social and spiritual" fronts.
"We know that the terrorists are regrouping, adapting and recruiting," he said. "We all need to intensify our cooperation to fight terrorism."
Indonesia, the world’s most populous Muslim nation, is a key front in the war against terrorism in Southeast Asia.
Militants from the al-Qaeda linked Jemaah Islamiyah network have launched a series of bloody strikes against Western and Christian targets in the country since 2000, including two attacks on Bali island that killed more than 220 people, mostly foreign tourists.
Jemaah Islamiyah is also blamed for attacks in the Philippines and failed plots elsewhere in the region.
Police in Indonesia, Malaysia, Singapore and the Philippines have arrested scores of its alleged members in recent years, but intelligence officials say the group is still capable of carrying out more strikes.
Earlier in Manila yesterday, a regional security analyst said a Muslim militant group comprised of converts which has links to Jemaah Islamiyah poses the biggest security threat to the Philippines.
The Rajah Solaiman Movement (RSM) is composed of Filipinos who worked in the Middle East and later converted to Islam and should be considered a "terrorist Islamist" group, said Scott Harrison, former CIA station chief in Manila and currently managing director of the Pacific Strategies and Assessments Inc.
Filipino intelligence agents arrested the founder of the RSM in October along with eight supporters.
They were charged with plotting to bomb high-profile targets, including the US Embassy in Manila, and of assisting the Abu Sayyaf and the Jemaah Islamiyah (JI) groups.
The Abu Sayyaf and the JI are linked to al-Qaeda and are on the US government’s list of foreign terrorist organizations.
The JI has been blamed for the 2002 and 2005 bombings in Bali, Indonesia which left over 200 people dead while the Abu Sayyaf is tagged with being behind the Philippines’ worst terrorist attacks in recent years.
While the arrests have partially broken up the RSM, the group remains "the most potentially dangerous element of terrorism in the Philippines because of their Christian background," Harrison told the Foreign Correspondents Association of the Philippines. — With AFP