This increasingly diverse inmate population in part reflects an increasingly diverse, multi-ethnic and pluralistic Canadian society, he said.
But there are certain groups, notably aboriginals and blacks, that are "disproportionately over-represented" in federal penitentiaries and their numbers are "growing at alarming rates," correctional investigator Howard Sapers said in a statement.
Over the past decade, growth in the inmate population has been almost exclusively driven by an increase in jailed visible minorities, he said.
This segment of the prison population has increased by 75 per cent during the period, and now exceeds 6,000 of a total incarcerated population of approximately 15,000.
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"These are disturbing trends that raise important questions about equality and our justice system in Canada," said Sapers.
He noted that 9.5 per cent of federal inmates today are black, yet black Canadians account for less than three per cent of the population of Canada.
Similarly, aboriginals represent a staggering 23 per cent of federal inmates yet comprise only 4.3 per cent of the total Canadian population.
In a report, Sapers noted widespread "discriminatory behaviour and prejudicial attitudes" by guards reported as "common experiences" by visible minority inmates.
The data showed that black inmates incurred a disproportionate number of in-prison charges, and were more likely to be involved in use of force incidents.