Prince Charles and his wife Camilla are to acknowledge the abuse of thousands of Indigenous children by Canada's school system during a visit next month, his office said on Tuesday.

The Prince of Wales, 73, and Duchess of Cornwall, 74, will take part in "a solemn moment of reflection and prayer" shortly after arriving at St John's, Newfoundland and Labrador, on May 17.

The meeting at a so-called Heart Garden on the grounds of Government House will be "with Indigenous leaders and community members in the spirit of reconciliation", said Charles' deputy private secretary Chris Fitzgerald.

"Heart Gardens are in memory of all Indigenous children who were lost to the residential school system, in recognition of those who survived, and the families of both," he added.

Pope Francis earlier this month apologised to Canada's Indigenous peoples for a century of abuse committed at Church-run residential schools.

Charles' mother, Canada's head of state Queen Elizabeth II, last year sent a message of support to mark the country's first National Day for Truth and Reconciliation.

The queen joined Canadians "to reflect 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".

Some 150,000 Indigenous, Metis and Inuit children were forcibly enrolled from the late 1800s to the 1990s in 139 residential schools across Canada, spending months or years isolated from their families, language and culture.

Many of the children were physically and sexually abused by headmasters and teachers, and thousands are believed to have died of disease, malnutrition or neglect.

A truth and reconciliation commission concluded in 2015 that the failed government policy of assimilation amounted to "cultural genocide".

Discoveries of 1,300 unmarked student graves at several of the former schools since last May -- with ongoing searches expected to uncover many more -- has shocked Canada.

Governor General Mary Simon, the first Indigenous woman to serve as the queen's representative in Canada, called the pope's apology a "historic and emotional day for Indigenous peoples across Canada".

The royals' three-day visit is to mark the queen's Platinum Jubilee year and will also see them visit the Northwest Territories on the other side of the vast country.