An investigation ordered by President Benigno Aquino III into the killings that occurred Jan. 6 concluded the victims were summarily executed and there was no shootout as claimed by the security personnel.
Presidential spokeswoman Abigail Valte said Aquino directed Justice Secretary Leila de Lima to file a criminal and administrative complaint after reading the report by the National Bureau of Investigation.
"The conclusion is that no shootout occurred," de Lima said. "The victims were summarily executed and all indications point to a rubout."
She said the NBI will file a criminal complaint with state prosecutors, who will decide whether there is enough evidence against the 21 police and 14 soldiers before filing the case in court.
The investigation found that the killings were a plan by the police colonel who led the security force at the checkpoint, Hansel Marantan, to eliminate his rival in the illegal gambling operation. Local newspapers have reported that Marantan was a protector of an illegal numbers game called "jueteng."
Marantan has denied any wrongdoing.
De Lima said the police and soldiers also face charges of obstruction of justice for tampering with evidence, including repositioning the weapons of the victims and submitting guns that were not used in the killings for forensic analysis, in an attempt to show there was a shootout when investigators found none.
The 13 victims were in two SUVs that were peppered with bullets at the checkpoint in Quezon province's Atimonan township, about 120 kilometers (75 miles) southeast of Manila. Some victims, including three police officers and two air force personnel, were armed but were not able to fire their weapons, investigators said.
Police corruption has long been a major problem in the Philippines, hampering the justice system and undermining confidence in authorities.