Up to eight local and foreign JI suspects on Sunday escaped the raid, but left behind residues of what the authorities suspected could be a chemical carrying the tetanus bacteria, Lieutenant General Rodolfo Garcia said.
"It's being analysed by chemical forensic experts," the deputy chief of staff told a news conference in Manila.
Police also seized documents, including "one that details some bio terror manuals or something to that effect," he said.
JI's Number Two
The raid was on an apartment in the city of Cotabato, on southern Mindanao island, where a man described by Philippines authorities as JI's number two, Indonesian Taufiq Rifqi, was arrested two weeks ago.
A week ago police shot dead another Indonesian JI member, fugitive bomb-maker Fathur Rohman al-Ghozi, also on Mindanao.
Cotabato police investigator, Felipe Napoles, said Sunday's raid turned up "bomb-making material, electronic components and gadgets, diagrams for homemade bomb-making and Christmas light wiring," as well as computer diskettes.
"Foreign-looking men had been frequenting the house"
Police briefly detained the landlord, Lolito Adanza, for questioning but later released him without charges.
Adanza told police that Filipinos had rented the apartment, but "foreign-looking men had been frequenting the house," superintendent Napoles said.
"Jemaah Islamiyah operates here and the arrest of Taufiq Rifqi proves it," Garcia said.
Rifqi was arrested at a Cotabato hotel in early October, but the authorities only confirmed his detention two weeks later.
Defence Secretary, Eduardo Ermita, said up to 40 Mindanao-trained JI foreign fighters may be in the Philippines.
JI is a Southeast Asian Islamic network blamed for a series of bombings in the region, including last year's Bali blasts that killed 202 people.
Manila's allies have expressed concern in recent days about JI's activities on Mindanao, a large island that borders Indonesia and Malaysia and has been a hotbed of a decades-old Muslim separatist movement.