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She is accused of having abetted the illegal drug trade in the New Bilibid Prison when she was justice secretary from 2010 to 2015.
Police arrived at the doorstep of her Senate office minutes before 8 a.m. local time, as demonstrators waved banners in her support reading "one for Leila."
"I will go with them voluntarily," de Lima told reporters. "It is my honor to be jailed for what I am fighting for," she added, as her supporters shouted "laban Leila (fight Leila)" in the background.
"If they think that by jailing me, I will turn my back on my principles, they are mistaken. Instead, they have encouraged me more to pursue truth and justice," de Lima said in a statement.
De Lima has consistently insisted she is not involved in the illegal drug trade.
Arrest ordered
Duterte ordered de Lima arrested Thursday in what supporters say is a politically motivated vendetta.
A judge in the Muntinlupa Regional Trial Court on Thursday afternoon found "sufficient probable cause for the issuance of the Warrants of Arrest" against de Lima.
Rafael Marcos Ragos and Ronnie Palisoc Dayan were also arrested. Ragos worked as a Bureau of Corrections chief and Dayan was de Lima's former aide.
"This sets a dangerous precedent for the government to arrest and incarcerate individuals that it perceives as its enemies, on the basis only of mere allegations and without due process," said Sen. Risa Hontiveros in a statement.
Allegations of payoffs
Duterte first raised the allegations against de Lima in a speech in August.
She's accused of receiving payoffs from convicted drug lords who were able to continue their illegal operations from behind bars while she was justice secretary. The prison facility is managed by the Bureau of Corrections, an arm of the Department of Justice.
Ragos and Dayan are accused of asking for money from jailed drug lords to fund de Lima's senatorial bid last year.
Duterte: De Lima must 'face the music'
Felons from the prison facility have directly linked de Lima to the penitentiary drug trade. But de Lima said the government pressured those convicts to testify and have an "ax" to grind against her.
As justice secretary, de Lima conducted a raid at the New Bilibid Prison maximum security area that shocked the nation, revealing a luxurious lifestyle of high-profile inmates who are now among the witnesses against her.
De Lima has said she will take legal action to protect herself from what she says is political persecution.
Last week, Duterte said he was confident the Justice Department's case against de Lima was airtight. He said the senator "will have to face the music" and the charges.