Journalists and activists call for prosecutions over massacre in the south.
Prosecutors allege armed followers of the Ampatuan clan murdered 57 people including the wife and two sisters of their political rival, Esmael Mangudadatu.
Also among those killed were journalists, lawyers and other civilians.
Edilberto Jamora, the prosecutor in the case, said Ampatuan Jr was only being charged with 25 murders so far because authorities had only processed 25 death certificates.
Ampatuan Jr is accused of leading the killings to prevent Mangudadatu from challenging him in the May 2010 race for governor of the province.
Ampatuan’s father, together with six other clan members, have been summoned to submit affidavits in the investigation into the massacre in Maguindanao province.
They are also suspects in the investigation, but have not been charged.
The Ampatuans control many local positions in the southern province of Maguindanao and have hundreds of armed followers there.
Prosecutors said the killings were carefully planned and that more charges will follow.
Jovencito Zuno, the chief state prosecutor, said at least one witness alleged that the Ampatuan clan had gathered in the patriarch’s mansion in the provincial capital of Shariff Aguak days before to plan the killings.
|Philippines clan violence|
Around 250 prominent political families exist in every province across the Philippines with members in various levels of government.
Competition for regional political power is fierce and can be violent, especially in the lead-up to elections.
In Mindanao the central government has sometimes armed these clans to help it fight Communist and Muslim separatists.
The policy has also led to murders and disappearances that go undocumented, but that are estimated to number in the thousands.
One research group, the Asia Foundation, says 83 per cent of the 50,000 families made homeless by clan violence are in Maguindanao province, scene of Monday’s massacre.
The graves were dug in advance and a backhoe positioned to bury the bodies, prosecutors said.
Police said earlier they took into custody six officers, including the Maguindanao provincial police chief and his deputy.
Two inspectors among them were allegedly seen during the massacre with Ampatuan Jr, said Erickson Velasquez, head of the criminal investigation division.
The massacre has also embarrassed Gloria Macapagal Arroyo, the Philippine president, who has longstanding ties with the Ampatuans.
Arroyo has declared a state of emergency in Maguindanao and a neighbouring province, ordering troops and police to confiscate unlicensed weapons and restore order.
But few think the measures will go far enough in the region which is notorious for its political warlords who have been outside the central government’s control for generations.