Immigration, Customs, finance, justice, police and military officials from the three countries also attended the two-day conference while fellow Association of Southeast Asian Nations (ASEAN) members Brunei and Thailand sent observers, Foreign Affairs Undersecretary Lauro Baja said.
"The initiative is meant to complement the ASEAN process, which is aimed to put into immediate motion countermeasures that would attack these nefarious activities that threaten our region and our particular corner of it," Baja told reporters.
The meeting is also a "recognition and validation of the expectation of the international community for the three countries to immediately address (terrorism)," Baja said.
He warned that the region had to deal with the "sophisticated machinery" of terrorist organizations, stressing that individual countries should lose no time in crushing budding terrorist organizations in their backyard.
The Sept. 11 terror attacks in the United States "drove home the point of how vulnerable we are ... to the real, imminent, destructive and evil" danger of terrorism, Baja said.
"We cannot afford to be complacent. That we forego two days of this holiday season to work on this agreement is an eloquent testimony to the importance and to the urgency we attach to this subject," Baja stressed.
The three countries share a common sea border frequently used by pirates and terrorists in evading pursuing troops. Last year, the Abu Sayyaf Muslim gunmen from the southern Philippines raided two Malaysian resorts and seized 21 mostly foreign tourists.
Security officials here said the group could have also smuggled firearms to Muslim separatists in Indonesia.
The Abu Sayyaf, which the US and Philippine governments have linked to Osama bin Ladens al-Qaeda network, currently hold an American couple and a Filipina nurse from a kidnapping spree that began in May.
The Philippines, Malaysia and Indonesia are members of ASEAN along with Brunei, Cambodia, Laos, Myanmar, Singapore, Thailand and Vietnam. Pia Lee-Brago