Canada on Thursday commemorated a century of injustices against its indigenous populations in the first ever National Day of Truth and Reconciliation, following shocking discoveries of hundreds of unmarked graves at former indigenous residential schools.

"It is a day to reflect. It is a day to honour. It is a day to grieve. It is a day to mourn. It is a day to shed tears," Algonquin elder Claudette Commanda told a ceremony in front of parliament attended by thousands.

Gatherings and marches were also held in communities across Canada.

The occasion had been observed unofficially as Orange Shirt Day since 2013 to promote awareness of what a truth and reconciliation commission branded "cultural genocide" of Canada's indigenous peoples.

It was inspired by a former student, Phyllis Webstad, who recounted how at six years old she was stripped of her clothes, including a new orange shirt bought by her grandmother, on her first day of residential schooling.

The government elevated the day to a statutory holiday this year following the announcement of discoveries of more than 1,200 unmarked graves at several former indigenous residential schools since May.

"The tragic locating of unmarked graves at former residential school sites across the country has reminded us of not only the impacts of colonialism and the harsh realities of our collective past, but also the work that is paramount to advancing reconciliation in Canada," Prime Minister Justin Trudeau said in a statement.

On the eve of this day, he said Canadians must acknowledge the "terrible injustices" committed against the country's indigenous people.

"Until we understand as a country that each one of our stories is all of our story there cannot be truth, there cannot be reconciliation," he said in front of parliament illuminated at night in orange.

On Thursday, messages of support poured in, including from Queen Elizabeth II who said she joins Canadians in reflecting "on the painful history that Indigenous peoples endured in residential schools in Canada, and on the work that remains to heal and to continue to build an inclusive society."

From the late 19th century to the 1990s, some 150,000 First Nations, Metis and Inuit children were forcibly enrolled at the schools across Canada.

Students spent months or years isolated from their families, and were physically and sexually abused by headmasters and teachers who stripped them of their culture and language.

Thousands are believed to have died of disease, malnutrition or neglect. Many more became detached or alienated.

Today, while searches continue for more grave sites, those experiences are blamed for a high incidence of poverty, alcoholism and domestic violence, as well as high suicide rates, in indigenous communities.

"We can all understand what it might feel like to lose a child. We can all understand what it might feel like to lose our parents, families (and) communities," said Jenny Sutherland, whose grandmother went to a residential school.

"This is the space we need to step into today," she urged a crowd dressed in orange and traditional indigenous garments in Ottawa and those watching on television nationwide.

The residential schools set up by Ottawa and run by the Catholic Church were "more than an aggressive assimilation tactic by our government, but an act of war," she commented.

"We as indigenous people are not supposed to be here."

In Montreal, Michelle Martel said she joined a march to commemorate her grandparents and other relatives who attended residential schools, but also "for my children and my grandchildren for reconciliation, so that we can live together in peace one day."

Paul Bode, who is non-native, said he attended the march to show solidarity with indigenous people because "I continue to benefit from what has been produced by this injustice" -- in reference to lands taken from tribes for settlement by colonisers.

Last week, the Catholic Church apologized "unequivocally" for abuses at the schools and acknowledged "the historical and ongoing trauma" inflicted on indigenous peoples.

Indigenous leaders, however, are still awaiting a mea culpa from Pope Francis himself, as well as the release of school records.

Marie-Pierre Bousquet, an indigenous studies professor at the University of Montreal, told AFP: "It's important that this story not just be an indigenous story, but one that is shared by all."

"This is a time of coming together for the entire Canadian population" to reflect on the past and "show solidarity in moving towards reconciliation," she said.