"The Catholic Church as a whole in Canada was not associated with the Residential Schools, nor was the Canadian Conference of Catholic Bishops (CCCB)", the group said Thursday. Trudeau said many are "wondering why the Catholic Church in Canada is silent, is not stepping up".
The band's announcement of the discovery has touched off countrywide grief, anger about the children's treatment at the schools and calls for more searches at other such institutions.
From 1893 to 1969, a Catholic congregation called the Missionary Oblates of Mary Immaculate ran the Kamloops school, which was once Canada's largest.
Trudeau says it's going to be important for Catholics across the country to reach out to bishops and cardinals on this issue.
Sudbury churches are planning a commemoration this afternoon to honour children who lost their lives in Canada's residential school system. Each Diocesan Bishop is autonomous in his diocese and, although relating to the Canadian Conference of Catholic Bishops, is not accountable to it.
The Conference said on its website that each diocese is separate and responsible for its own actions. He says he expects the church to be part of the important process of truth and healing and to make school records available.
The school was run by the Catholic Church between the late 1800s and the 1960s.
He says the government has tools available to compel the church to provide these documents, but he indicated he does not want to resort to taking the institution to court.
The Anglican, Presbyterian and United churches have apologized for their roles in the schools, while the Vatican has released an official "expression of sorrow" on behalf of the Catholic church.
"It's something we are all still waiting for the Catholic Church to do", Trudeau said.
"Already in 1991, Canadian Catholic Bishops and leaders of men and women religious communities had issued a statement that "We are sorry and deeply regret the pain, suffering and alienation that so many experienced" at the Residential Schools".
Between 1831 and 1996, Canada's residential school system forcibly separated about 150,000 children from their homes.
A national Indian Residential School Crisis Line is available for anyone affected by residential schools.