Their fate has been a festering wound in many of Canada's more than 600 native communities, with allegations of mishandled murder investigations or failures to look into missing persons cases.
The previous Conservative administration had long resisted calls for an inquiry, seeing the disproportionate number of deaths and disappearances as resulting from domestic violence.
Former prime minister Stephen Harper has said these tragedies were not due to a sociological phenomenon but rather were crimes to be investigated by police.
"It is time for a renewed nation-to-nation relationship with First Nations peoples," he told an assembly of chiefs in Ottawa.
The relationship should be "one that understands that the constitutionally guaranteed rights of First Nations in Canada are not an inconvenience, but a sacred obligation," he said.
The national chief of the Assembly of First Nations, Perry Bellegarde, welcomed the pledge.
"Chiefs, it is indeed a new day on Turtle Island," he said, using a native name for North America.
"But we also have much work to do. Our 400 years of shared history has brought us a massive gap in the quality of life between indigenous peoples and the rest of Canada."
Bellegarde had called on natives to come out for the first time en masse to vote in the last elections that swept Trudeau's Liberals into power.
It was an effort to sway public policy after years of inaction on native issues, including gross poverty and desperation in many aboriginal communities that breeds abuse, suicide and crime.
Native leaders and activists have been calling for an inquiry for more than a decade, since dozens of prostitutes went missing in Vancouver's seedy Downtown Eastside and were later determined to have been victims of a serial killer.
A 2014 report and an update this year by the Royal Canadian Mounted Police identified 1,049 murdered and 172 missing aboriginal women dating back to 1980.
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