"All the conspirators are answerable as co-principals regardless of the extent or degree of their participation," prosecutors said in a lengthy report outlining their case against the group.
But only 11 of those charged are in custody, with most of the others still on the run nearly three months after the massacre.
The unprecedented election-related killings in Maguindanao on November 23 last year shocked the country.
In all, 57 people died in the massacre, apparently carried out to prevent Esmael Mangudadatu, from the rival clan, challenging the Ampatuans' control of the province in a gubernatorial election.
Among those killed were 30 journalists and their staff who were going to cover the filing of Mangudadatu's candidacy papers.
Mangudadatu, who said he had received death threats from the Ampatuans, sent his wife and other female relatives and supporters to the provincial capital in the hope that his rival would not harm the women.
Copies of the indictment papers showed witnesses had identified some members of the Ampatuan family as among those who shot at close range most of the massacre victims.
Ampatuan Sr has denied any involvement and said the charges have been fabricated.
He also denied a witness's statement saying he allegedly told his son, "You know what to do" with the people in the convoy.
The clan patriarch was an ally of Gloria Macapagal Arroyo, the Philippine's president, who was indebted to the Ampatuans after they delivered crucial votes for her in the 2004 election.
Arroyo's party expelled the Ampatuans shortly after the massacre.
Before Tuesday's indictment, only Datu Andal "Unsay" Ampatuan Jr, the clan leader's son, had been formally charged.
The Ampatuans are also facing separate charges of rebellion for allegedly mobilising armed resistance against the government in the wake of the massacre.