Mrs. Arroyo said the JI, which experts say espouses the establishment of a radical pan-Islamic state in Southeast Asia, has surpassed local insurgents, including communist rebels, as the foremost security concern.
The President ordered military and police authorities to place in their order of battle the Jakarta-based terror group, and issued corresponding directives yesterday to Armed Forces chief of staff Gen. Narciso Abaya and Philippine National Police chief Director General Hermogenes Ebdane Jr.
There is now a need to "update our priorities," Mrs. Arroyo said noting that the government was to resume peace talks with the Moro Islamic Liberation Front (MILF) while the communist New Peoples Army (NPA) and the Abu Sayyaf were already a spent force.
"We are elevating the JI into our official national threat spectrum," Mrs. Arroyo said in a statement.
"We are going into a more focused campaign against the JI, complete with a new order of battle and targets for domestic and transnational intelligence in concert with our allies," she said.
She issued the directives in her speech before the annual luncheon press conference with the Foreign Correspondents Association of the Philippines (Focap) held yesterday at the Hotel Dusit in Makati.
Recent arrests of top JI leaders have exposed that the groups plans "are both deadly and far-ranging" and could threaten the stability of the region, Mrs. Arroyo said.
Her statement came a day after she announced the arrest of Taufek Refke, a 23-year-old self-proclaimed Indonesian who is allegedly the JIs No. 2 man in Mindanao.
Refke, who was arrested in Cotabato City last Oct. 2, is believed to have trained under JI bomb expert Fathur Rohman al-Ghozi.
Al-Ghozi earlier escaped from detention at the Philippine National Police (PNP) headquarters and after three months as a fugitive, was subsequently gunned down by security forces in a town near Cotabato City last Oct. 12.
Security officials said some 40 other JI militants, most of whom are believed to be Indonesian, are on the loose in Mindanao, where a massive manhunt has been launched.
Police said Refke has confessed under interrogation of being the JIs "finance and liaison officer" responsible for funding deadly bombings in the South. His arrest led government forces to an alleged JI hideout in Cotabato City, where they recovered bomb-making equipment and radical Islamic literature.
Some of Refkes estimated 30 accomplices, most of them said to be Indonesians, escaped when security forces raided a suspected JI safehouse in Cotabato last Sunday.
On the other hand, the Indonesian embassy expressed their concern yesterday over the Philippine governments denial of its request for access to Refke.
Embassy spokesman Andang Pramana stressed the need to verify the nationality of Refke and his supposed cohorts in the JI, pointing out that the "name and image" of Indonesians had been tarnished by claims.
Authorities have claimed that Refkes cohorts in the JI are "mostly Indonesians."
Pramana said Refke is not in the list of Indonesian nationals in the country but the embassy has specifically requested access to verify his citizenship.
"We are asking to be given access to him (Refke) since we have been reading from media reports that he is an Indonesian. But up to now, we are not allowed. We have not yet been invited to see him," Pramana said.
Pramana said the embassy remains unsure if Refke is indeed an Indonesian as earlier claimed by the suspect. "Maybe the Philippine authorities are also not sure about his nationality, that is why they have not yet asked us to have any access or communication with him," he added.
Justice Secretary Simeon Datumanong earlier said the police and military have yet to file charges of illegal possession of explosives against Refke even if he is an undocumented alien.
Interior and Local Government Secretary Jose Lina also admitted the only case that can be lodged against Refke is his alleged violation of immigration laws.
Immigration Commissioner Andrea Domingo told yesterday the Department of Justice (DOJ) that undocumented Indonesians in Mindanao are now being registered.
"We have launched a program to have them registered but we were overran by hostilities. But we will resume that," she said.
Domingo added Indonesian nationals need not worry about harassment or possible mass deportation because the Philippine law enforcers are ordered to focus on suspected terrorists.
The military, for its part, said the capture of Refke and his admitting to be the finance officer of the JI cell in the country resulted in the groups disarray.
On the possibility that the remaining JI terrorists sought refuge in areas controlled by the MILF, the military cited an agreement with the Muslim guerrillas to turn them over to the authorities for prosecution.
The 12,500-strong MILF is the countrys main Muslim force that is negotiating peace with the government.
It has denounced links to the JI, which authorities said is the Southeast Asian arm of Osama bin Ladens al-Qaeda network.
The Abu Sayyaf, on the other hand, is a small group of Islamic militants wanted for bombings and kidnappings in the southern Philippines and Malaysia, while the NPA is the armed wing of the underground Communist Party of the Philippines.
Mrs. Arroyo warned the MILF to keep to the terms of a ceasefire pact it signed with Manila, under which it promised to turn over to security forces any JI members and other terrorists who seek shelter in its camps in southern Mindanao island.
"I want the MILF specifically to stand clear of the JI, because we have special teams on the trail of the JI fugitives," Mrs. Arroyo told the Focap forum.
"I dont want the manhunt to get in the way of the peace talks," she said, adding that intelligence units were preparing a list of known JI leaders to be transmitted to the MILF.
During the Focap open forum yesterday, the President clarified that the AFP and PNP will continue to address the internal threat groups even as the order of battle now included the JI as priority target.
"And now we have more hard information about the JI, and we have more coordination with the other countries, then we can concentrate on the JI now," she said.
Asked if her government would allow a more direct US role in the anti-terror campaign, Mrs. Arroyo said it would, as long as it was "to the extent allowed by the Constitution."
The Constitution bars foreign troops from participating in active combat roles in the country. US Special Forces, however, have been training and equipping Filipino soldiers against the Abu Sayyaf for the past two years. There are also plans to expand the joint military training in other troubled areas in Mindanao.
On reports that the US will help track down the JI militants, a convenor of a non-governmental organization in Mindanao said this will justify US intervention in the countrys internal affairs.
Dr. Robinson Montalba of InPeace said such reports will be traumatic to the people of Mindanao.
"Reports that the US military is helping the local security forces track down Jemaah Islamiyah (are) only a basis to justify the intervention of the Americans into Philippine affairs," he said. - With reports from Aurea Calica, Pamela Samia, AFP