Assistant prosecutor Augusto Gonzales said he found "no cogent reason to disturb or reverse our findings of probable cause" against the suspects.
Gonzales rejected the claims of the four suspects that they were tortured into admitting their alleged participation in the twin blasts.
He argued that the suspects swore to their affidavits in full view of the media, giving them an opportune time to shout that they were tortured, as they alleged.
The four suspects — Esmael Mamalangkas, Ting Idar, Esmael Akmad and a 17-year-old boy — were rounded up in Cotabato City a few days after the explosion at the Sasa wharf here.
The fifth suspect, Tohami Bagundang, still has to file his counter-affidavit to the charges of multiple murder and multiple frustrated murder.
Charged along with them were about 200 leaders of the Moro Islamic Liberation Front, led by their chairman, Hashim Salamat.
Last March 4, a powerful bomb ripped through a crowded waiting shed outside the Davao International Airport. Another explosion jolted the city on April 2 at a row of food stalls in front of the passenger terminal at the Sasa wharf.
President Arroyo subsequently placed the city under a "state of lawlessness" and created the Task Force Davao to secure the city against terrorist threats.
The local Regional Trial Court has issued warrants of arrest against Salamat and the other MILF officials. The Malaysian government has sought the lifting of the warrants to pave the way of the resumption of peace negotiations with the separatist group.