The three suspects, Abdul Basit Hapilon, Abdul Manap Mentang and Abdul Rahman Camili, however, all remain at large.
Mentang and Camili were actually arrested last year in Metro Manila and Davao del Norte, respectively, for their alleged role in the twin bombings that struck this southern city in early 2003 that left 39 people dead and over 200 others wounded.
However, a local judge released them early this year after the Intelligence Service of the Armed Forces of the Philippines (ISAFP) failed to substantiate the charges against them.
Mentang had reportedly confessed to authorities that a JI member named Zulkifli trained him in urban terrorism nine years ago.
The court, however, dismissed the cases against him and Camili in connection with the 2003 bombings when the ISAFP failed to authenticate the video footage supposedly showing them admitting the crime.
Hapilon is said to be a relative of Abu Sayyaf leader Isnilon Hapilon.