It was only shortly before Indian Residential Schools were being shut-down that the churches who ran them began to administer apologies for the horrific crimes that took place. The formal speeches/statements of apology are listed below.

On Wednesday June 11, 2008 at 3:00 p.m. (Eastern Daylight Time), the Prime Minister of Canada, the Right Honourable Stephen Harper, made a Statement of Apology to former students of Indian Residential Schools, on behalf of the Government of Canada.

Anglican Church of Canada
The Anglican Church of Canada’s apology was delivered by then-Primate Michael Peers to the National Native Convocation in Minaki, Ont., Friday, Aug. 6, 1993.
Text: http://www.anglican.ca/relationships/trc/apology

Presbyterian Church in Canada
The confession of the Presbyterian Church as adopted by the General Assembly was delivered on June 9th, 1994.
Text: http://www.presbyterian.ca/ministry/canada/nativeministries/confessions

United Church of Canada
The United Church of Canada apologized for the Indian Residential School system twice, however, only one was accepted formally.

1986 – Apology spoken by the Right Reverend Robert Smith at the 31st General Council of The United Church of Canada

1998 -The Moderator of the United Church apologized to Canada’s First Nations peoples for the church’s complicity in the operation of Indian Residential Schools in Canada.

1986 and 1998 apologies in .pdf format

Indian Affairs and Northern Development
On January 7, 1998, The Honourable Jane Stewart (Minister of Indian Affairs and Northern Development) delivered a Statement of Reconciliation.

Text: http://ccmlab-test.uwaterloo.ca/node/89

Roman Catholic Church
After a meeting in 2009 that included the National Chief Phil Fontaine (AFN) and Pope Benedict XVI, the Pope expressed sorrow for Residential School survivors.
Video: http://www.cbsnews.com/video/watch/?id=6317916n