MANILA - (UPDATE) The Ombudsman on Thursday said it affirmed criminal charges against former President Benigno "Noynoy" Aquino over the deaths of 44 police commandos in a botched anti-terrorism raid in 2015.

Aquino's motion to drop charges of usurpation of authority and violation of the anti-graft and corrupt practices act was denied, the Ombudsman said in a statement.

• Aquino to face trial for Mamasapano carnage: Ombudsman

"While a President of the Republic is certainly possessed with broad discretionary powers, the exercise thereof must not, however, be done in violation of a law, much less when such exercise constitutes a crime," the Ombudsman said.

The former president will meet with his legal team on the Ombudsman's decision, according to his spokeswoman, Abigail Valte.

The Ombudsman said it "clearly" found probable cause against the 57-year-old former leader for allowing then suspended national police chief Alan Purisima to oversee the assault on a suspected terrorist lair in the remote town of Mamasapano, Maguindanao.

The operation succeeded in killing Malaysian bomb-maker Marwan, but also sparked fierce clashes with Muslim rebels that left 44 police Special Action Force troops and at least 18 insurgents killed.

The bloodbath also scuttled peace talks between the Aquino government and the Moro Islamic Liberation Front, the country's largest Muslim rebel group.

A deal to end the decades-long insurgency would have been a centerpiece achievement for Aquino, who relinquished his post to President Rodrigo Duterte in June last year.

The Ombudsman also insisted on charging Aquino with graft and usurpation of authority instead of reckless imprudence resulting in multiple homicide, as this carried a higher penalty of up to 15 years in jail from just 4 years and 2 months.

The Volunteers Against Crime and Corruption had filed a separate appeal insisting on the reckless imprudence charge, which the Ombudsman also denied.

Aquino will be the third former president since Joseph Estrada to stand criminal trial.

Former President Joseph Estrada was convicted of plunder but was pardoned by his successor, Gloria Macapagal-Arroyo. Estrada was accused of receiving millions in illegal gambling kickbacks.

Arroyo was also charged with plunder over the alleged misuse of state lottery funds but the charge was dismissed due to lack of evidence and she was freed from detention last year.