A police search of the house of Mohammad Guindolongan in that southern city yielded several bomb components and a fragmentation grenade that was kept in the ceiling of his kitchen.
Guindolongan, alias Kim or Abu, is believed to be a member of the special operations group of the Moro Islamic Liberation Front (MILF).
The charges were filed after the explosives were found in Guindolongan’s residence, at Barangay 23-C along Quezon Blvd. in Davao City.
Guindolongan, who is still at large, is also facing murder and frustrated murder raps in a Manila court.
Meanwhile, Camp Crame sources said witnesses have identified two suspects responsible for the bombings at Plaza Ferguson and the LRT coach, where most of the casualties perished or were injured.
While the sources declined to identify the suspects, they claim they have verified that these two suspects are regular members of the MILF.
"We have at least six witnesses now under our custody who identified the LRT bomber, and another set of four witnesses who positively pointed to the suspect in the Plaza Ferguson bombing," the source claimed.
The police and military are conducting operations in Mindanao and other parts of the country for the possible arrest of the two suspects, they added.
"Statements of our witnesses, who claim to have monitored movements of the suspects we obtained from our Muslim contacts, (reveal) that the suspects were behind the deadly bomb blasts," they said.
A day before the carnage, one of the suspects allegedly arrived at Globo de Oro in Quiapo, Manila with specific instructions from MILF leaders to carry out the Plaza Ferguson bombing.
These developments, the sources added, will require that the PNP amend the charges they have already filed before the Department of Justice (DOJ).
The police had earlier filed multiple murder and multiple frustrated murder charges against Guindolongan, MILF chairman Hashim Salamat, vice chairmen Mohammad Al-Haj Murad, Ghadzali Jaafar, and Aleem Aziz Mimbantas; Safilla Unos, Ismael Abbas and several John Does.
But so far, police have only arrested taxi driver-operator Ismael Abbas, who is allegedly the MILF’s forward scout in Metro Manila.
Guindolongan, on the other hand, left for Manila on Dec. 28, or two days before the five deadly blasts that have so far killed 22 people and injured scores of others in various places in Metro Manila, police said.
Police claim the bombings were carried out by 12 mujahedeen, or fundamentalist fighters, reporting directly to Salamat and who were trained in a terrorist camp in Afghanistan.
The PNP is also probing claims that the Rizal Day bombings may be connected to the bombing of Christian churches in Indonesia over the Christmas holidays.
The Indonesian police had earlier said they are investigating claims that three suspects in a string of deadly bombings of Christian churches on Christmas Eve were trained in Afghanistan.
One of the suspects arrested by Indonesian police claimed that he and a second suspect, who was killed in one blast, as well as third man who remains at large, were taught how to make bombs between 1990 and 1992 in a mujahedeen camp in Afghanistan.
While Indonesian police refused to draw a direct link between terrorist groups in Indonesia and the Philippines, they claimed to have sent detectives to Singapore, Kuala Lumpur and Manila.
Lacson, for his part, said the PNP is certain that the bombings were carried out by the MILF.
"We are 100 percent sure that the bombings were carried out by the MILF," he said, adding that government troopers found a document on the spate of bombings in an MILF camp in November.
Last year, the MILF was also blamed for two mall bombings that killed one person and injured 24 others.
The military and police claimed the MILF was retaliating for the loss of its camps in a massive military operation in Mindanao.
Warrants of arrest were issued against Salamat and other MILF leaders but the government later suspended the warrants in a "confidence-building" measure to restart peace talks.
The police also arrested 26 Muslim residents of Maharlika Village in Taguig, claiming they were involved in the mall bombings but their lawyers said they were fall guys.
On January 3, military operatives raided a Muslim community in Barangay Culiat, Quezon City and hauled 18 residents to jail but later released 14 of the 18.
Armed Forces of the Philippines chief of staff Gen. Angelo Reyes said the other four will be charged with illegal possession of weapons after an assault rifle, a pistol and sachets of metamphetamine hydrochloride, or shabu, were seized in the raid.
The military and police response have prompted legislators to probe the capability of local authorities in handling bombing crises.
PNP operations Deputy Director General Jewel Canson, National Capital Regional Police Office director Chief Superintendent Edgar Aglipay, and Criminal Investigation and Detection Group-Metro Manila director Senior Superintendent Raul Bacalzo are set to appear on Tuesday before the House committee on public order.