Senator Leila de Lima, 57, a lawyer who has spent nearly a decade trying to link Duterte to death squads that have allegedly killed thousands of people, faces drug trafficking charges that could see her jailed for life.
"I have no plans of fleeing and I have no plans to go in hiding. I will face all these charges," a tearful De Lima told reporters at the Senate after a Manila court issued the arrest warrant.
She is accused of orchestrating a drug trafficking ring when she was justice secretary in the previous administration of Benigno Aquino.
But De Lima and her supporters insist she is innocent, and that the charges are trumped up to silence one of Duterte's most vocal and enduring critics.
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De Lima this week branded Duterte a "sociopathic serial killer" as she called for ordinary Filipinos to stand up in opposition to his drug war, which has seen more than 6,500 people killed since he took office eight months ago.
"Now the time has come again for us to be brave and stand up to another criminal dictator and his evil regime," De Lima said on Tuesday.
De Lima's Liberal Party, which ruled for six years under Aquino, voiced deep anger on Thursday at her imminent arrest.
"The Liberal Party reiterates that it condemns the political persecution of brave administration critic Sen. Leila De Lima," it said in a statement.