"This is something that everyone must monitor every step of the way," said Ramon Casiple, a political analyst with the Institute for Political and Economic Reform.
"What we are facing here is a very strong clan with very strong political connections and the capability to intimidate or even kill witnesses," he told the AFP news agency.
"This puts the justice system to a test, because past cases with heavy political overtones have never been satisfactorily concluded."
"At the end of the day, it's still politics talking. And these warlords will not go down quietly," he said.
One judge has already backed out from the explosive case, saying he feared for his life and there have been calls from prosecutors for the justice department to ensure the safety of witnesses.
Leila de Lima, the chairperson of the Philippines' Commission on Human Rights, told Al Jazeera that the country's department of justice was "doing what it can to ensure that the trial is run smoothly in order for the correct result to be announced".
"The public cannot accept anything less than a conviction for the perpetrators, and I think there would be unrest if the trial does not work out well"
Leila de Lima,
Philippines' Commission on Human Rights
"The public cannot accept anything less than a conviction for the perpetrators, and I think there would be unrest if the trial does not work out well," she said.
According to prosecutors, at least 10 witnesses have said Ampatuan Jr led 100 of his armed men in stopping a convoy carrying members of a rival political family and journalists on November 23.
Prosecutors allege they then murdered 57 people, including the wife and two sisters of political rival Esmael Mangudadatu.
The dead were systematically murdered and buried in shallow pits or dumped in grasslands just near the national highway in Maguindanao province, where Ampatuan Jr's father and namesake was governor.
Ampatuan Jr is accused of leading the killings to prevent Mangudadatu from challenging him in the May 2010 race to succeed Ampatuan Sr as provincial governor.
Ampatuan Sr as well as several other clan members were later arrested after martial law was imposed in Maguindanao and charged separately with rebellion.
The Philippine government continues to face accusations that it allowed warlords in the south of the country to run brutal fiefdoms for decades
Critics say this was further highlighted soon after the November massacre when allegations surfaced that the authorities in Mindanao were giving "special treatment" to four members of the Ampatuan clan while they were incarcerated
Police ordered an investigation after local media reported the detainees were allowed to use their mobile phones, had catered food and had a helper to clean their cells every day
Mindanao authorities denied the reports, saying the Ampatuans were not given special treatment but "special attention" due to the high profile nature of the case
In her report to congress defending the imposition of martial law, Gloria Arroyo, the president, said those massacred bore "marks of despicable torture, contempt and outrageous torment".
She also said that clan followers had threatened to carry out attacks if their patrons were arrested.
The Brussels-based International Crisis Group said last month, however, that Arroyo was partly to blame for the massacre because she had allowed a "local despot to indulge his greed and ambition".
Ampatuan Sr had controlled Maguindanao province for most of the past decade and was grooming his son to take his place as governor in national elections scheduled for May.
Ampatuan Sr's influence and power grew because Arroyo allowed him to maintain a 3,000-strong heavily armed militia as part of a government strategy to contain Muslim separatist insurgents in the south.
In exchange for the support, Ampatuan also helped deliver votes from the province to Arroyo and her candidates in the 2004 election.
The shocking crime forced her to cut political ties with the clan, but critics say the Ampatuans may still hold enough political power to avoid severe penalties.
"I have serious doubts about the whole exercise," Harry Roque, the chairman of the advocacy group CenterLaw Philippines, who is also a private prosecutor representing the slain journalists, said of the case.
"There is a genuine fear from the victims' families that justice will not be served," he said.