Former Philippine President Benigno Aquino is to be charged over a botched "anti-terror" raid that left 44 elite policemen dead in 2015, a special government prosecutor said on Friday.

In a statement to reporters in Manila, Ombudsman Conchita Carpio Morales said she had ordered the filing of criminal charges against Aquino for his liability in the Mamasapano massacre, in which 44 Special Action Force commandos were killed in a clash with members of the Moro Islamic Liberation Front, the Bangsamoro Islamic Freedom Fighters, and a private armed group.

Morales said Aquino will be charged with usurpation of authority under the Revised Penal Code as well as under the Anti-Graft and Corrupt Practices Act.

Also accused in the case are former Philippine National Police chief Alan Purisima and former Special Forces Director Getulio Napenas, the statement said.

According to Morales, the investigation showed that Aquino was aware that Purisima had been preventively suspended, pending a graft indictment, but still allowed him to take part in planning the Mamasapano raid, reported news website Inquirer.

"Certainly a public officer who is under preventive suspension is barred from performing any public functions and from meddling into the affairs of the government," she said.

Morales said it is because of Aquino's influence and permission that Purisima was able to participate in the raid's planning despite his preventive suspension.

Napenas and Purisima were also formally charged with usurpation of powers and graft for bypassing the police chain of command in the botched operation.

Morales said that text messages between Aquino and Purisima showed that the suspended police chief played a major role in the botched operation and blamed it on Aquino's "complicity and influence."

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In his response, Aquino said he did not directly participate in the planning and execution of the operation. He said he was only briefed on the broad strokes of the plan and there was no need for him to approve it.

His spokeswoman Abigail Valte said Aquino was consulting his lawyers.

The former president, who served from 2010 until 2016, has been credited with restoring a semblance of political and economic stability in the Philippines and signing a peace deal to try to end a decades-long Muslim separatist rebellion.