The precedent-setting case involves an 18-year-old on the Pictou Landing reserve in Nova Scotia and his principal caregiver, his mother — who herself suffered a debilitating stroke in 2010.
Last month the Federal Court ruled that Ottawa was wrong to cover only a fraction of the cost of care for Jeremy Meawasige, who suffers from cerebral palsy, autism, spinal curvature and hydrocephalus, a debilitating accumulation of spinal fluid in the brain.
The court found that the government is obliged to uphold "Jordan's Principle" — a 2005 agreement that First Nations children should get the public assistance they need, regardless of jurisdictional fights between levels of government over who should pay.
The ruling was hailed at the time as a step toward ensuring aboriginal children get equal access to essential government services.
A brief notice of appeal filed by the federal Justice Department says the court erred in its interpretation and application of Jordan's Principle .
Lawyer Paul Champ, who represents Meawasige's mother, Maurina Beadle, and the Pictou Landing band, called the appeal "shameful."
"I understand that the Pictou Landing case is a big precedent, but is it really one they should fight?" Champ said in an email.
"I think it looks terrible for the government to be seen opposing Jordan's Principle and equality for disabled First Nations children."
A departmental spokeswoman for Aboriginal Affairs said the government continues to make the health and safety of First Nations a priority.
"The government of Canada will work with the Pictou Landing First Nation for the reimbursement of home-care costs incurred related to Mr. Meawasige's need, however following careful consideration we have decided to appeal the decision," Genevieve Guibert said in an email.
"Canada is committed to working with the community and the province to ensure appropriate supports are in place for the family moving forward."
Justice Leonard Mandamin found that Ottawa was wrong to cover only $2,200 a month toward Meawasige's care, which costs the Pictou Landing band council about $8,200 a month.
"The only other option for Jeremy would be institutionalization and separation from his mother and his community," said the judgment.
"Jordan's Principle is not to be narrowly interpreted."
Jordan's Principle is named after Jordan River Anderson, a Manitoban who died in hospital in 2005 as governments argued over who should pay for home care services.
The House of Commons unanimously voted in favour of adopting the principle. The Federal Court noted that government departments publicly declared they would respect Jordan's Principle in their policies.
Jean Crowder, the NDP critic for aboriginal affairs, called the government appeal "very disappointing" and said her understanding is that the ruling would impact a relatively small number of severely disabled First Nations youth.
"They should let the ruling stand," Crowder said in an interview.
"The amount of money they're going to spend on the appeal would pay for Jeremy's care many times over."