After more than 13 years of legal wrangling, the court ruled last month that Metis and non-status Indians are indeed "Indians" under a section of the Constitution Act, and therefore fall under federal jurisdiction.
On Wednesday, Aboriginal Affairs Minister John Duncan told the House of Commons that the ramifications of the decision demand a ruling from a higher judicial authority.
"Given that the Federal Court decision raises complex legal issues, it is prudent for Canada to obtain a decision from a higher court," Duncan said.
"After careful consideration of the decision, Canada has filed an appeal, and it would be inappropriate to comment further as the case is before the courts."
Among other things, Duncan said, the services provided to Aboriginal Peoples by the federal government have to be affordable.
"The Harper government continues to work in partnership with aboriginal organizations and provincial governments to enhance the economic opportunities for Metis and non-status Indians," he said.
"Our government must ensure that programs and services to Aboriginal Peoples are fiscally sustainable."
The case dragged on for years before the ruling last month.
The Congress of Aboriginal Peoples and several Metis and non-status Indians took the federal government to court in 1999, alleging discrimination because they were not considered "Indians" under a section of the Constitution Act.
The congress expressed disappointment Wednesday in the government's decision to challenge the ruling.
"I have to say that I am truly disappointed, but at the same time not surprised," said National Chief Betty Ann Lavallee.
"This decision comes at the expense of Metis and non-status Indians, who for far too long have been the 'Forgotten Peoples' of Canada struggling for recognition of their constitutional rights, equality, dignity, self-worth and fairness."
The federal government has been trying to have the case thrown out since it was first launched in 1999, she added.
"We anticipated that this struggle would continue, and we remain confident and committed in our position."
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