Joel Reyes, the former governor of the western island of Palawan, has been accused of masterminding the 2011 killing of Gerry Ortega, who used a radio show he hosted to frequently accuse Reyes of massive corruption.
Ortega was shot dead while shopping in the capital of Palawan, one of the country's biggest islands and a popular tourist destination, famed for its lush forests and pristine landscapes.
But it has also suffered from illegal logging, mining and fishing. Ortega had accused Reyes of corruption linked to alleged environmental crimes on the island.
The Supreme Court's ruling -- dated March 29 but only published on Sunday -- was the latest development in the long-running case.
Reyes and his brother Mario, who was also implicated in Ortega's murder, went missing in 2012 after an arrest warrant was issued against them.
They were caught in Thailand in 2015.
Reyes was released from jail in 2018 after a court dismissed criminal charges against him.
Government lawyers, however, appealed the decision and the charges were reinstated nearly two years later.
The Supreme Court then issued a stay on the order for Reyes' re-arrest and the resumption of his trial while it heard his plea for reconsideration.
In the ruling released Sunday, the Supreme Court rejected the appeal and ordered a Palawan court to arrest him and resume the trial.
Ortega's widow Patty told AFP that the family welcomed the decision, saying it "restores our faith that, one day, we will find justice".
Reyes' lawyer could not be reached.
While there have been many cases of environmental activists and journalists being murdered, the brazen killing of Ortega shocked the Philippines.
Reyes ran for his old job in last year's elections but lost. His brother Mario, a former mayor, also failed in his re-election bid.
The Palawan trial court hearing the case could not be reached for comment on Sunday.
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