Vice chief of staff Lieutenant General, Rodolfo Garcia, said on Tuesday examination of powders found at an apartment in Cotobato on the southern island of Mindanao showed they did not contain the tetanus bacteria as originally reported.
"Our finding is, there were no chemical or biological agents found," Garcia told reporters in the capital Manila.
Police spokesman Senior Superintendent Leopoldo Bataoil also said Garcia's claims that a “bio terrorism” manual had been found were not substantiated. He said only "notes on bio terror, bio toxic materials" were discovered.
Garcia's “revelations” on Monday had raised fears that Jemaah Islamiyah (JI) , which has been accused of the bombings on the Indonesian island of Bali last year, may have been planning to launch a biological attack in the region.
President Gloria Arroyo issued a statement on Tuesday, calling on the police and military to be accurate in their reporting "so that the public will be informed of the facts and not be unduly alarmed by sensationalised reports."
"Our finding is, there were no chemical or biological agents found"
She also has called on the public to remain calm and cooperate with the authorities who are tracking down suspects from JI, which wants to create an Islamic state across Southeast Asia.
Garcia said bomb-making material - including explosive powders, watches and disassembled rechargeable batteries - had been found at the hideout.
Police said numerous documents including several books on speaking English, computer manuals and Muslim literature, with titles such as Jihad in the Philippines and Commander Muslim Army had also been recovered.
The raid in Cotabato came after a man described by Philippines authorities as JI's number two, Indonesian Taufiq Rifqi, was arrested there two weeks ago.
The Philippines' allies in the south east Asian region 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.