Former President Benigno Aquino III. Joseph Vidal, Malacañang Photo Bureau

MANILA (2ND UPDATE) - Former president Benigno "Noynoy" Aquino III will face criminal trial over a botched anti-terror raid in Maguindanao province in 2015 that left 44 police commandos killed, the Ombudsman said Friday.

Ombudsman Conchita Carpio-Morales ordered Aquino charged with usurpation of authority and violation of the anti-graft and corrupt practices act, the investigating body said in a statement.

Also included in the charges were Aquino's former national police chief, retired Director General Alan Purisima and the former chief of the police Special Action Force, retired Director Getulio Napeñas.

Aquino will appeal the indictment, his former deputy spokesperson Abigail Valte said.

"Former President Benigno Aquino III received the order of the Ombudsman this afternoon and is currently studying it with his lawyers, with the end view of filing a motion for reconsideration," she said.

"An initial reading shows that there may have been a misappreciation of some facts surrounding the incident, leading to some erroneous conclusions. He will seek to clarify the same through the motion for reconsideration," she said.

The Ombudsman cited Aquino for "criminal negligence," saying he participated in the "flawed" planning of a police commando raid to capture Malaysian terror suspect Zulkifli bin Hir alias Marwan.

Marwan was killed during the assault in the remote town of Mamasapano, but an ensuing clash between the SAF and Muslim rebels in the area resulted in scores of fatalities.

The Ombudsman also said Aquino was "fully aware" that Purisima was serving out a suspension over an alleged anomalous firearms deal when "Oplan Exodus" was planned.

"In other words, Purisima would not have been placed in such a position of continuing to conduct himself, in relation to Oplan Exodus, in a manner as if he was not under preventive suspension at the time from his position as PNP Chief if not for the complicity and influece of President Aquino," the Ombudsman said in the complaint.

The bloodshed sparked public outrage and set back the timeline of a peace accord between the government and the Moro Islamic Liberation Front.

Read the full complaint here: