"All three countries are prepared for a JI buildup," Mrs. Arroyo said.
"We are strengthening legal and operational procedures to deal with terrorists as well as drug syndicates," she said.
Intelligence officials have said that while the JI has been weakened by a series of arrests, it still continues to plan attacks in a bid to establish its dream of an Islamic superstate in the region.
The JI, believed to be the Southeast Asian arm of Osama bin Laden’s al-Qaeda network, is blamed for the bomb attacks in the Indonesian island resort of Bali that killed more than 200 people last October.
Mrs. Arroyo earlier acknowledged that the JI, along with Muslim extremists, has been working to establish a "radical enclave" in the region and has carried out small clandestine training operations, including in Mindanao.
But Mrs. Arroyo said Monday that a concerted effort among the countries concerned could eventually defeat the JI.
"With enough teamwork, we can avert any plan of sowing terror in the region and finally win this war," she said.
Mrs. Arroyo made the assurance following the June 21 report made by Armed Forces chief Gen. Narciso Abaya to Defense Secretary Angelo Reyes of possible resumption of JI terror attacks.
US officials reportedly assuaged their Filipino counterparts that the JI "is not capable of large scale operations" following the arrest of their key leaders.
Intelligence officials here have also linked the JI to the Moro Islamic Liberation Front (MILF), principally blamed for bombings and attacks that left nearly 100 dead in Mindanao early this year.
A self-confessed Indonesian member of the JI, Fathur Rohman al-Ghozi, has admitted to police that JI leaders Hambali, alias Riduan Isamuddin, and Faiz Abubakar Bafana, had financed the December 2000 bombings in Metro Manila that killed 22.
Hambali, said to have been the operations chief of the JI, remains at large while Bafana has been jailed in Singapore.
Mrs. Arroyo said the close coordination with Malaysian and Indonesia authorities has kept terrorism in check.
"We have worked closely with Indonesia in checking and intercepting their nationals who are involved in this activity," Mrs. Arroyo said.
"In the case of Malaysia, they are involved in the peace process which serves the interest of curbing the spread of terrorist cells," the President added. –With AFP