Zeid, addressing the UN Human Rights Council (HRC) assembly in Geneva, has called on the Philippine government to uphold global human rights obligations after expressing grave concern over Duterte "open support for a shoot-to-kill policy" regarding suspects.
During the budget vote, house speaker and Duterte ally Pantaleon Alvarez criticised the commission, saying it was "useless" and "not doing its job".
"Many human rights defenders who are the honor of their country face a growing number of death threats, and I call on the government to ensure they are accorded full protection and the right to freedom of expression and peaceful assembly without reprisals", he said.
Congressman Edcel Lagman said 32 minority lawmakers opposed the measure during the debate at the second reading. He said Duterte's supporters were "virtually imposing the death penalty on a constitutionally created and mandated independent office".
The commission was last year awarded nearly (749 million pesos) $15 million for its annual budget, and had initially requested for a budget of 1.72 billion pesos ($34 million) this year.
Congress voted to slash that to just 1,000 pesos, a huge cut from the 2017 budget of 749 million.
The budget requires Senate approval before it becomes final - which opponents say is likely, because President Duterte has a majority in the two chambers. Lawmakers have voted to give the Commission on Human Rights an annual budget of $20.
The CHR, which had been investigating killings related to the drugs trade, initially requested a budget of $42million, reports the BBC.
"If the Philippines Congress is looking for public money being wasted, damaging and hurting the Philippines society, this is it". "All drug killings are subject to investigations", he added.
United Nations human rights chief Zeid Ra'ad Al-Hussein hits President Rodrigo Duterte over his policy on killing suspects.
"I am also shocked by President Duterte's threat to bomb schools for indigenous children in the southern Philippines, which he said were teaching children to rebel against the government", Zeid said.
CHR head, Chito Gascon, said the measly budget was an attempt to force his resignation.
"The principal reason why I can not resign my office is that to do so is to weaken the institution itself", Gascon said.
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