"This is a tragedy that we have to come to grips with," he said Thursday in response to the justice-related recommendations in the report by the Truth and Reconciliation Commission of Canada.
Tuesday's report documents the history of the residential school system in Canada.
It lists 94 recommendations to address the legacy of residential schools, including calls on the federal government to "commit to eliminating the overrepresentation of aboriginal people in custody."
MacKay said Ottawa invests money in what he called "an aboriginal justice strategy" that includes money for youth programs aimed at keeping kids out of trouble with the law.
"Those efforts and those investments will continue but it will require a whole-of-government approach," he said.
MacKay was in Montreal to highlight security announcements made earlier in the day by Prime Minister Stephen Harper.
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