The court granted the provisional release of Sajid Ampatuan on Monday, ruling against the government which wants him kept in prison along with more than 100 other suspects in the 2009 slaughter.
"He was released yesterday. He is free to travel anywhere in the Philippines," Alan Moral, an official from the regional court handling the case told AFP. He is, however, barred from leaving the country while on bail.
Moral said the defendant had paid an 11.6 million-peso (USD 262,000) bond to be freed on bail.
He is a son of Andal Ampatuan Snr, a Muslim political clan leader accused of masterminding the massacre in his southern bailiwick of Maguindanao province on November 23, 2009.
Nine clan members are among 111 people detained for the mass killings that prosecutors allege were part of a bid to quash an election challenge from a rival clan.
Thirty-two media workers were among those killed, making the attack one of the deadliest ever recorded globally against journalists.
State prosecutors have opposed the clan members' bail bids amid fears their release could intimidate witnesses.
"We're aghast, we're frustrated," Harry Roque, a lawyer for some of the victims' families, told AFP.
"We are apprehensive that the Ampatuans could regain influence," he added, noting the ruling came just over a year ahead of the May 2016 national and local elections.
Andal Ampatuan Snr had ruled Maguindanao as governor for about a decade under the patronage of then-president Gloria Arroyo, who had funded a private army for the clan as a buffer against Muslim separatist rebels.
"I already gave instructions to the (state prosecution) panel... To avail of the proper remedy as soon as possible," she told reporters.
Moral said the state has yet to complete the presentation of its witnesses and evidence, adding to concerns the trial could take many more years.
He said the court has yet to rule on the bail petitions of the other clan members, while more than 70 other murder suspects remain at large.
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