Trudeau's Liberal Party came to power in November last year promising to rebuild ties with Canada's 1.4 million aboriginals, or First Nations, many of whom are mired in poverty and crime and suffer from bad health.
"Why do you allow the first people of this land to endure and live in Third World conditions?" asked one female student, referring to "the acts of genocide" aboriginals had been subjected to for centuries at the hands of settlers.
The question prompted loud applause at the high school for indigenous students in Saskatoon, in the western province of Saskatchewan. The 20-minute question-and-answer session was shown in a live webcast.
Trudeau, who sounded more defensive than he has been in other Q&A sessions across Canada, responded that the federal government could not fix the problem alone and needed to work with First Nations.
"Quite frankly ... this is a stain and a scar upon, not just our sense of who we are and our morality as Canadians, but on the kind of country we need to be building," he said.
Increased militancy and unhappiness among the aboriginal population has prompted protests against a number of pipeline projects that would cross First Nations territory.
Some of the students expressed impatience, pressing Trudeau on what improvements they would see this year.
"Why are the promises you made when you got elected prime minister taking so long?" one student asked.
Trudeau replied that the government was like a big ocean liner and turning it around would take some time.
In a federal budget this March, Ottawa said it would spend an extra $C8.37 billion ($NZ9.5 billion) over five years to help tackle the worst of the problems facing aboriginals.
Earlier this month a cabinet minister said Ottawa was working on a plan to help address a wave of suicides in remote indigenous communities.
