Manny Pacquiao -- a senator and former boxing star -- moved a motion on Monday night to declare the chairmanship of the committee on Justice and Human Rights vacant which passed by 16 votes to four, removing former head Senator Leila de Lima.
She will be replaced by Senator Richard Gordon as chairman.
The committee is currently investigating more than 1,000 confirmed drug-related killings
by police in the Philippines since President Duterte took office in June.
Last week, a former death squad member made allegations to the committee, including that Duterte used an uzi submachine gun
to kill a member of the Justice Department when the President was still mayor of Davao City.
Duterte's office has denied all accusations made about him during the hearings.
Shortly before she was removed De Lima said she was "not the one who has tainted the image of the Senate and the country; what truly destroys this is the continued killings in our country."
In a statement
, Human Rights Watch denounced her removal as "an apparent reprisal for her inquiry into the surge of killings" linked to Duterte's war on drugs.
"The Senate vote to remove the chair of the Committee on Justice and Human Rights is a craven attempt to derail accountability for the appalling death toll from President Duterte's abusive 'war on drugs'," said Phelim Kine, deputy Asia director for HRW.
"The Senate is imperiling the Philippine public by covering up allegations of state-sanctioned murder rather than exposing them."
'I will not stop'
Speaking on Monday night after De Lima's removal, President Duterte said he would not stop his war on drugs no matter what the committee reported.
"I don't care if there are 1,000 hearings everywhere," he said. "I will not stop ... I will really kill all the drug lords."
Earlier on Monday, Senator Alan Peter Cayetano had hit out at De Lima in a speech on the Senate floor, saying she had a "bias against the President's crusade."
"Is it wrong to be biased against the President? No, because this is a democracy ... So why am I standing here? Because while you have rights, you also have responsibilities," he said.
During Cayetano's speech, De Lima walked out.
Duterte, De Lima longtime rivals
President Duterte has harshly criticized Senator De Lima in the months since she began to chair the inquiry into extrajudicial killings.
During a speech in August
he called her an "immoral woman" and a "robber," accusing her of having an affair with her driver and using him to collect drug payoffs.
In return, De Lima said: "We are both professionals, the president and I... I hope he doesn't resort to those foul means," according to local media.
Duterte and De Lima have been longtime rivals, after the senator tried to tie him to the "Davao Death Squad" (DDS), a paramilitary vigilante organization, when she was head of the Commission on Human Rights under the former administration.
De Lima herself is also facing a congressional inquiry this week. The House of Representatives, which is dominated by allies of Duterte, is examining the proliferation of illegal drugs at the New Bilibid Prisons while she was justice secretary.
Convicted drug lords are among the 12 inmates who will testify against De Lima, according to current justice secretary Vitaliano Aguirre.
"I was warned already about their evil design and insidious moves, such as fabrication of evidence," De Lima