MANILA — The official in charge of prosecuting government misdeeds in the Philippines on Friday ordered that criminal charges be filed against former President Benigno S. Aquino III for a botched assault in 2015 on a Muslim rebel camp that left 44 police commandos dead.

The official, Conchita Carpio Morales, the ombudsman of the Philippines, said there was probable cause to charge Mr. Aquino, his police chief and the head of the commando unit that carried out the operation. The attack caused the president’s popularity to sink and also derailed peace talks with Muslim insurgents.

Relatives of the dead officers accused Mr. Aquino and the officials of “criminal negligence,” saying that they had approved the operation despite knowing that the police chief, Alan Purisima, had been suspended in an unrelated corruption case.

Mr. Purisima appeared to have been allowed to participate and run the operation under Mr. Aquino’s oversight, “thereby giving pseudo legal power to a suspended official,” Ms. Morales said.