The Catholic Church does not deny its involvement in Residential Schools. Nor does it deny the abuses, including the deaths, that took place there.
The Catholic orders and organizations responsible for organizing and running the Residential Schools have apologized for doing so. For example, this statement was made in 1991 by the Missionary Oblates of Mary Immaculate, the religious order that ran the most number of Residential Schools:
We wish to apologize for the part we played in the setting up and the maintaining of [Residential Schools]. We apologize for the existence of the schools themselves, recognizing that the biggest abuse was not what happened in the schools, but that the schools themselves happened . . . that the primal bond inherent within families was violated as a matter of policy, that children were usurped from their natural communities, and that, implicitly and explicitly, these schools operated out of the premise that European languages, traditions, and religious practices were superior to native languages, traditions, and religious practices. The residential schools were an attempt to assimilate aboriginal peoples and we played an important role in the unfolding of this design. For this we sincerely apologize.
We wish to apologize in a very particular way for the instances of
physical and sexual abuse that occurred in those schools. . . .
Finally, we wish to apologize as well for our past dismissal of many
of the riches of native religious tradition. We broke some of your
peace pipes and we considered some of your sacred practices as pagan
and superstitious. This too had its origins in the colonial mentality,
our European superiority complex, which was grounded in a particular
view of history. We apologize for this blindness and disrespect. [...]
Recognizing that within every sincere apology there is implicit the
promise of conversion to a new way of acting. We, the Oblates of
Canada, wish to pledge ourselves to a renewed relationship with Native
Peoples which, while very much in line with the sincerity and intent
of our past relationship, seeks to move beyond past mistakes to a new
level of respect and mutuality
A general apology was made in 1991 by Canadian Catholic bishops stating:
“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.”
For reference, the Residential Schools system was created and run by the Canadian Federal Government, which set up the system and enforced the attendance of aboriginal children. It handed over the running of the schools themselves to various organizations, mostly churches. Different Catholic Dioceses and other Catholic organizations ran about 60% of Residential Schools, including the Kamloops one where the unmarked graves were discovered.