Though the motion still requires another reading and Senate approval, opponents say it is likely to be passed, as Duterte enjoys a supermajority in the two chambers.
However, activists say the prime targets have been users and small-time peddlers and accuse police of executing thousands of people.
"We are deeply concerned with the UNHCR (UN High Commissioner for Human Rights) Zeid Ra'ad Al Hussein's sweeping statements during the UNHR Council's 36th session, citing instances bereft of factual basis".
House speaker Pantaleon Alvarez, a close ally of Duterte, said in a television interview that the CHR deserved a small budget for being a "useless" body.
The UNHRC is 47-member-state inter-governmental body responsible in promoting and protecting all human rights worldwide.
The CHR had a budget of 749m pesos (£11m) in 2017 and requested roughly double that for 2018. It investigation in particular on some of the 3.800 deaths of drug addicts or drug traffickers suspected were shot by police and the security forces in operations that are "legitimate" according to them. "(Extra Judicial Killings) have reportedly become a verb in some communities - as in 'he was EJK-ed", the Commissioner added.
Despite its flaws, she added, Karapatan still sees "the recent attempts of the Duterte administration to de facto abolish the CHR as a unsafe step that undermines available mechanisms for redress for human rights violations in this so-called democratic form of government".
UN Security Council to vote on weakened North Korea sanctions
The new United Nations sanctions are an attempt to starve the country of fuel and income for its weapons programmes. The measures stopped well short of an oil embargo that Washington had been seeking, but which is opposed by China.
The UN Special Rapporteur on extrajudicial killings Agnes Callamard called the move "reprehensible and unconscionable".
This "war on drugs" has triggered a spate of violence in the country, which was marked by the death in circumstances unexplained of thousands of other people. "If the Philippines Congress is looking for public money being wasted, damaging and hurting the Philippines society, this is it". The move has been heavily criticized since thousands have been killed. "As innocent youth and urban poor are cut down nightly in the streets, the assault aims to send a chilling message against those opposing the U.S. -Duterte fascist regime's mass murder and martial law".
Nicknamed "the Punisher" for his lethal approach to policing, Duterte has previously threatened to abolish CHR, a body he despises for its criticism of his killing campaign, although he later said his threat was a "joke".
Thousands have been killed since President Duterte launched the anti-drug crackdown past year.
He added: "On pretext, asking me to resign would lead to essentially making the institution forever at the mercy of politics".
On the issue on bombing indigenous schools, Abella said it would be better to focus on the Duterte administration's efforts for their education, claiming their program will receive P130.43 million to support nearly three million indigenous students.
Human rights advocates hope senators will restore the agency's current budget.