About 900 suspected drug traffickers have been killed since Duterte came to power after winning a May election on a vow to wipe out drugs and warning traffickers they risked death if they did not mend their ways.
The United Nations this week called on the government to protect all people from targeted killing and extrajudicial executions.
“The president ... decries the attribution of killings to the Philippine government,” presidential spokesman Ernesto Abella said.
“This is simply unfair, especially to the hardworking men and women in uniform who risk their lives and limbs to win the war against drugs.”
Police have said many of the dead drugs suspects were shot while resisting arrest or were killed by rival gang members.
A staunch critic of the president, senator Leila de Lima, will next week start a congressional inquiry into the killings, summoning top police and anti-narcotics officials to explain the “unprecedented” rise in the body count.
Duterte responded by warning legislators not to interfere with his campaign, saying they could be killed if they blocked efforts aimed at improving the country.
“Be careful with me because when I say I will do it for my country, I will do it even if I have to kill you or be killed in the process,” he said on Wednesday, directing his statements to opposition senators.
This week, he also told police officers not to be intimidated by a suggestion from de Lima that the United Nations might be asked to look into the surge of extrajudicial killings.
“Do not investigate us as if we are criminals,” Duterte said in a speech to police.
“Let the police do their duty.”