"I also mentioned human rights, the rule of law, and specifically extrajudicial killings as being an issue that Canada is concerned with," Trudeau told reporters in Manila, recounting a conversation with Duterte.
"I impressed upon him the need for respect for the rule of law."
Ahead of a regional summit in the Philippines, rights groups had urged world leaders to challenge Duterte over what they say are gross abuses.
The 72-year-old overwhelmingly won elections last year vowing to eradicate drugs through a campaign that would see up to 100,000 people killed.
Since he took office, police have reported killing 3,967 people in the crackdown.
Another 2,290 people have been murdered in drug-related crimes, while thousands of other deaths remain unsolved, according to government data.
Rights groups say Duterte may be presiding over a crime against humanity.
On Tuesday, Trudeau said Canada had earned a reputation for discussing human rights and the rule of law with other nations.
Asked how Duterte responded, Trudeau said: "The president was receptive to my comments and it was throughout a very cordial and positive exchange."
"This is something that is important to Canadians, and it's important to the world and I will always bring that up," Trudeau said, referring to human rights.
The Canadian prime minister added he offered support to Duterte "as a friend to help move forward on what is a real challenge".
Duterte is hosting world leaders as the Philippines holds the rotating chair of the 10-nation Association of Southeast Asian Nations (ASEAN) bloc.
Trudeau's comments were a rare sour note for Duterte during a summit that has been largely silent on the issue.
Trump garnered headlines on Monday for his show of camaraderie with Duterte, a man who last week boasted of having personally stabbed someone to death as a teenager.
A Philippine presidential spokesman repeatedly insisted Monday that human rights had not come up during their summit talks, although the White House said they had done so "briefly".