Remembering the Children Website, includes a timeline and apologies of Church groups. The Indian Residential School were funded by the Federal government, but mostly run by various church denominations across Canada. Below is timeline history from the Assembly of First Nations that outlines the history of Residential Schools.
http://www.rememberingthechildren.ca/history/index.htm
Canada’s protestant denominations issued a joint paper outlining their apology in very specific terms. Click on the image below.

Source: The Anglican Church of Canada
Anglican Church of Canada operated many residential schools throughout Canada. Here is a link of their involvement. The Anglican Church of Canada issued it’s apology for involvement in Residential Schools on August 6, 1993. Here is the full text of their apology.
http://www.rememberingthechildren.ca/press/acc-apology.htm

OLD SUN INDIAN RESIDENTIAL SCHOOL (GLEICHEN, AB), P75-103 S7-184, 1945, General Synod Archives.

Source: United Church of Canada
The United Church of Canada also operated many residential schools throughout Canada. Here is a link of their involvement. The church issued it’s apology for involvement in Residential Schools in 1986. Here is the full text of their apology.
http://www.united-church.ca/beliefs/policies/1986/a651

Source: Presbyterian Church in Canada
The Presbyterian Church of Canada also operated many residential schools throughout Canada. The church issued it’s apology for involvement in Residential Schools on June 9, 1994. Here is the full text of their apology.
http://www.rememberingthechildren.ca/press/pcc-confession.htm

Catholic Church of Canada
The Catholic Church of Canada also operated many residential schools throughout Canada. The church issued it’s apology for involvement in Residential Schools on March 13-15, 1991. Here are some details on their acknowledged apologies.