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Aboriginal Affairs Minister Bernard Valcourt speaks during Question Period on Jan. 29, 2013.CHRIS WATTIE/Reuters

The federal Conservative government is taking legal action to force dozens of Catholic organizations that ran aboriginal residential schools to pay their full share of a compensation package promised seven years ago to the schools' former students.

Aboriginal Affairs Minister Bernard Valcourt said in a letter this month that the Catholic groups have not fulfilled their part of the Residential Schools Settlement Agreement.

"Although the Catholic Entities have already paid a lot of what they owe under the settlement agreement, it is the government of Canada's position that they continue to have outstanding obligations," Mr. Valcourt wrote in a letter dated Jan. 15 to Ronald Kidd, a Vancouver man who had expressed concerns. "Aboriginal Affairs and Northern Development Canada is pursuing the Catholics in a legal setting to have the balance paid," Mr. Valcourt wrote.

The settlement was meant to be a resolution to the tragic legacy of the church-run schools, in which tens of thousands of aboriginal children were taken from their families, often to live in situations of deprivation. At least 3,000 died and many more were subjected to emotional and physical abuse.

While the government paid the lion's share of the compensation, the churches were also required to make reparations.

The Anglican, Presbyterian and United Churches have met their obligations.

But when the settlement was being negotiated in the early part of the previous decade, the Roman Catholic church – considered one of the richest organizations in the world – successfully argued that it was not "one entity" capable of being sued. Individual Catholic groups that had a direct hand in the schools – mostly communities of nuns and individual dioceses – were left to pay the bill.

Under the agreement, those entities were responsible for a combined $79-million.

They agreed to raise $25-million for the Aboriginal Healing Foundation, an organization created to help survivors of the residential school system, and to provide up to $25-million in services to former students. And they agreed to pay an additional $29-million in cash – $16.6-million of which was to go to the healing foundation. But they have given the foundation just $15-million of that final amount, leaving $1.6-million unpaid.

Michelle Perron, a spokeswoman for the Aboriginal Affairs department, said the government filed a court application in December to settle the matter. It is tentatively scheduled to be heard in June.

Mike DeGagne, the former executive director of the Aboriginal Healing Foundation, who still acts as its adviser, said the $1.6-million being contested in court is just part of what the Catholics have failed to pay under the settlement agreement. They have raised almost nothing of their $25-million fundraising obligation, and supplied less than half of the $25-million in services that were promised, he said.

Neither the lawyer for the Catholic entities nor the designated spokesman for the Canadian Conference of Catholic Bishops responded to questions from The Globe and Mail.

Mr. DeGagne praised the efforts of the government to hold the Catholics to account.

"Under the agreement, the healing foundation has no standing to pursue its own receivables. We couldn't chase the church and make them pay. So the federal government is obliged to do it and they are doing an excellent job," Mr. DeGagne said. "But it's like blood from a stone."