The explosion was first reported to be due to an accidentally ignited LPG tank from Luk Yuen Noodle House.

[7] As the investigation continued four days after the incident, authorities favored the possibility that the blast was caused by an accident and not a terrorist attack.

The most probable cause, according to authorities, was the accumulation of methane gas in the building's septic tanks and as well as other combustible materials in its basement.

[11] On January 10, 2008, Chief Superintendent Luizo Ticman announced that criminal cases of "reckless imprudence resulting in multiple homicide, physical injuries and damage to property" were to be filed against engineers Arnel Gonzales, Jowell Velvez, and Marcelo Botenes of the Ayala Property Management Corporation, and Candelario Valqueza of the Makati Supermarket Corp.; engineer Clifford Arriola, Joselito Buenaventura, Charlie Nepomuceno, Jonathan Ibuna, and Juan Ricafort of Marchem Industrial Sales and Service Inc.; for violation of the Fire Code: engineer Ricardo Cruz, operations manager of Metalline Enterprises and its foreman, Miguel Velasco; gross neglect of duty causing undue injury: Makati Fire Station Senior Fire Officer 4 Anthony Grey, SFO2 Leonilo Balais, Senior Inspector Reynaldo Enoc, and Chief Inspector Jose Embang Jr.; Makati Fire Station chief - "for simple neglect of duty-for failure to review and validate before issuing fire safety inspection certificate.

The Multi-Agency Investigation Task Force final report detailed that the 1st blast was a methane explosion at 1:31 PM as the "gas accumulated after knee-deep water, diesel, human and kitchen waste at the mall's allegedly poorly ventilated basement was left unattended for 76 days"; the 2nd blast was "a diesel vapor explosion at 1:32 PM; the National Bureau of Investigation "identified the possible source of ignition" - the motor control panel of waste pumps two and three at the basement; rise in temperature caused by the methane gas triggered the 2nd explosion.

[14] On January 16, 2008, Kit Collier, an International Crisis Group consultant and international terror and insurgency expert, told foreign media members at a forum in Makati that he doubted the delayed final report of the PNP's findings that Glorietta 2 blast was due to a gas explosion.

Malaysian expert Aini Ling, commissioned by Ayala Land Inc.'s (ALI) investigation, stated in her report, that a bomb caused the explosion, due to RDX traces at the blast site.

Meanwhile, Justice Secretary Raul M. Gonzalez announced a preliminary investigation on the criminal complaints filed by police.

[19][20] The day after the blast, normal operations continued in Glorietta after engineers inspecting the remaining parts of the mall found them structurally sound.