In comments to journalists moments before police detained her, Senator Leila de Lima declared she was innocent of drug trafficking charges that could see her jailed for life and vowed to keep speaking out against Duterte's "repression".
"It is my honour to be imprisoned for the things I am fighting for. Please pray for me," de Lima told reporters outside her Senate office.
"As I have been saying all along, I am innocent. There is no truth to the charges I benefited from the drug trade, that I received money and that I coddled drug convicts.
De Lima, 57, had sought refuge at the Senate on Thursday night after avoiding police when they tried to arrest her at her home.
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She slept in her Senate office overnight then gave herself up to armed officers in flak jackets who put her in a van and drove into morning rush hour traffic apparently towards police headquarters.
De Lima is accused of orchestrating a drug trafficking ring when she was justice secretary in the previous administration of Benigno Aquino.
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.
Amnesty International yesterday said that it would regard de Lima as a prisoner of conscience.
"The arrest of de Lima is a blatant attempt by the Philippine government to silence criticism of President Duterte and divert attention away from serious human rights violations in the 'war on drugs'," it said.
"The war on illegal drugs targets all who are involved and the arrest of an incumbent senator demonstrates the President's strong resolve to fight pushers, peddlers and their protectors," presidential spokesman Ernesto Abella said.