"The warning against the JI is well taken, but we believe this is old stuff and does not reflect the stable situation that is obtaining on the ground," Press Secretary Ignacio Bunye said.
Bunye also pointed out that the allegations that JI militants were being given refuge by some Moro Islamic Liberation Front (MILF) leaders in Mindanao have been properly addressed.
Though admitting reports of the JI presence in Mindanao, Bunye said its forces have been contained by authorities there.
Bunye said perpetual vigilance against terror has been the prime concern of the government and it has never discounted the threat posed by terrorists.
"Working with our allies, we have been gaining solid ground in uprooting homegrown and foreign terror cells within our territory, and we shall never put our guard down," Bunye said.
He stressed "President Arroyo has spared no effort to ensure that terrorists are kept at bay while communities are kept alert."
A noted regional security analyst, Dr. Rohan Gunaratna, revealed the other day that the JI currently has 100 foreign militants hiding in Mindanao who have trained an additional 400 to 500 fighters for new attacks.
Gunaratna, head of the Singapore-based International Center for Political Violence and Terrorism Research, also said the JI militants were being given refuge by rogue guerrilla leaders of the MILF.
In the three-day international experts’ conference on counterterrorism in Cebu that ended yesterday, Gunaratna urged Southeast Asian governments to launch joint military and intelligence operations against the JI to head off new attacks.
He said the Philippines, Malaysia and Indonesia should develop a "new platform" in its fight against the JI, and deploy joint forces to track down the extremists at their jungle bases.
Presidential chief of staff Michael Defensor added that Philippine security officials were aware of the presence of JI militants holding out in the dense jungles of central Mindanao as early as 2001.
"But as to how many they are, we don’t really know and they are indeed a security concern," Defensor said.
He said efforts to deny the presence of the JI in Mindanao would be futile and embarrassing for the government.
"There have been terrorist operatives and they may even number 100 but there have been continuous operations against them," Defensor noted.
He also downplayed insinuations that the MILF was giving refuge to the JI militants.
He said the claims against the MILF have been addressed by the government in the course of its peace initiatives with the Muslim secessionist group.
Defensor said President Arroyo had even praised the MILF for its efforts to contain terrorism in the southern Philippines.
National Security Adviser Norberto Gonzales said the government has been effective in addressing threats posed by terror groups in the region.
Gonzales stressed the war against terror groups like the JI has yet to be won.
"The Jemaah Islamiyah militants have been with us. What we can say is that this is a continuing threat. It is difficult to talk of numbers. So what my office will do is check these figures," Gonzales said.
He said security forces are able to neutralize the threat but stressed "the dynamics of terrorists are different."
"They can always regroup and it takes two or three of them to launch an attack. That is the reality of it," he said.
While the government has largely decimated the Abu Sayyaf rebel group, Gonzales said the JI is capable of resurrecting the bandit group and launch terror attacks anywhere in the country.
He said that even the Rajah Sulaiman Group of terrorists is not yet off of the country’s threat board.
"We are dealing with fanatical individuals and so it is actually not enough to dismantle their infrastructures. We have to capture all of them. They cannot be neutralized just like that," Gonzales said.
"While we have been effective in addressing these threats and arresting people, vigilance should be there," he stressed.
The JI has been blamed for the October 2002 bombings in the Indonesian resort of Bali which killed 202 people and for deploying suicide bombers in another attack on the resort island last year, killing 20 civilians.
The Abu Sayyaf, on the other hand, gained notoriety for kidnapping foreigners.
The bandit group is also blamed for the spate of bombings in Mindanao and Metro Manila, including the firebombing of a passenger ferry off Manila Bay in February 2004 in which over a hundred passengers perished.
Regional security officials admit the JI continues to operate jungle camps in Indonesia and in Mindanao, where they are training the Abu Sayyaf and other homegrown terrorists.
On the sidelines of the three-day anti-terror conference in Cebu on Saturday, Gunaratna revealed the existence of a JI faction led by Malaysian Noordin Mohammad Top.
He said Top’s faction is closely working with the remnants of the Abu Sayyaf. Another group led by Indonesians Umar Patek and Dulmatin is reportedly being sheltered by the MILF.
The three JI leaders are all accused of playing key roles in the Bali bombings.