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In a split 9-5 decision, with one justice abstaining, the Supreme Court rejected arguments that Marcos was unfit to be re-interred in the National Heroes' Cemetery in Manila.
The move was met with delight by supporters of the former dictator who had gathered outside the court, and outrage from thousands of protesters opposing them bearing banners reading "Marcos is no hero!" and holding placards calling for justice for the victims of martial law.
Shortly after his election in May, President Rodrigo Duterte announced plans to move the late dictator from his current resting place in a mausoleum in the family's stronghold of Ilocos Norte, in the Philippines' northeast.
Speaking Tuesday, Marcos' daughter Imee, governor of Ilocos Norte, said her father was a soldier, "and he wanted to be buried together with his men."
"The burial will be a simple, ordinary soldier's burial," she told CNN.
Edre Olalia of the National Union of People's Lawyers, one of the plaintiffs in the case, said the decision was a "big letdown" and vowed to file a motion for reconsideration with the court.
"The victims of the brutal and thieving dictator and those who have fought and are fighting all forms of tyranny and governmental abuse will not bury the memories, experience and lessons of that horrible period," he said in a statement.
In a statement, Philippines Vice President Leni Robredo, who was elected separately from Duterte and comes from an opposing political party, said she was "deeply saddened" by the court's decision.
"(The Marcos) family's refusal to take responsibility for atrocities of the regime is an insult to the Filipino people," she said, adding that the burial will "keep the wounds of the past unhealed."
Public interest
In October, Duterte said he hoped the court would decide "not on emotion" but on the "public interest."
Former dictator
Marcos fled the Philippines after a revolution in 1986 ended his decades as dictator. Many young Filipinos have little or no knowledge of Marcos and martial law and recent years have seen his family re-emerge on the political scene.
Ferdinand "Bongbong" Marcos Jr. narrowly lost the election for Vice President of the Philippines this year by just 0.64%.
The late dictator's widow, Imelda Marcos, has been elected four times to the House of Representatives, despite ongoing controversies over the huge sums of money she and her husband plundered from the country.