Abaya, who hastily visited Sulu to assess its security situation, confirmed the presence of JI operatives roaming the country.
"We have added the JI as a major terror threat to Philippine security because of a series of evidence that we have gathered and the series of arrests in the past years," he said after meeting with military commanders here.
Abaya cited last year’s arrest of Taufiq Rifqi, an Indonesian suspected of handling finances for JI operatives in the Philippines, and the killing of confessed member Fathur Roman al-Ghozi in October, three months after he escaped from a Camp Crame jail.
Abaya implored citizens to protect critical infrastructure by reporting suspicious activities.
"The reports about the presence of the JI in the country are true and our forces have been hunting them down," he said.
Abaya revealed the latest threat of the al-Qaeda-linked terror group to launch a series of bombing attacks was uncovered following the arrest of four of its local operatives who were training in Mindanao.
He said the suspects disclosed they were planning to bomb four shipping lines and other public places.
"This bombing threat is very serious because there are still some members of the JI who remain at large and we are doing something about this for their immediate capture," Abaya said.
He warned of the presence of the Indonesian-based Jemaah Islamiyah group in other areas of the country, but declined to say where.
"I can’t give you the details of the area because there is an ongoing operation," the military chief said.
Sammy Abdulgani, one of four suspected JI militants arrested last week by authorities, told his interrogators that one of his Indonesian JI trainors named Usman is moving around the Philippines.
Usman, he said, continues to supervise and provide funding to JI operations in the country.
Abdulgani also claimed the separatist Moro Islamic Liberation Front (MILF), which is holding peace talks with the government brokered by Malaysia, is linked with the JI.
The MILF denies any ties with terror groups.
Abaya has also ordered the Armed Forces to intensify operations against the Muslim extremist Abu Sayyaf group, notorious for kidnapping and beheading hostages.
Security officials believe the guerrillas, suspected of seizing two Malaysians and one Indonesian from a tugboat earlier this month near the Philippine border with Malaysia, are working closely with Jemaah Islamiyah.
In Barangay Culiat in Quezon City also yesterday, soldiers and police arrested 12 mostly Muslim men and women, including three suspected Abu Sayyaf members, during a raid on illegal drugs and weapons, officials said.
Authorities seized small amounts of suspected drugs, a rifle, two pistols, four grenades, ammunition and several kilograms of ammonium nitrate - a fertilizer ingredient that could be turned into explosives, the officials said.
Military spokesman Lt. Col. Daniel Lucero said Abu Sayyaf guerrillas have used and sold illegal drugs to raise funds for their operations.
Last month, the government announced it broke up a six-member Abu Sayyaf cell, allegedly trained by JI, that plotted a series of bombings in the Philippine capital.
One suspect allegedly admitted having planted a bomb that triggered a fire on a ferry, killing more than 100 people, in late February, police said.
In Manila, the government urged citizens in a full-page newspaper ad to report "any suspicious person or activity" to protect "critical infrastructures" such as oil depots, power plants, transportation, and government and commercial centers from possible terror attacks. — Roel Pareño