The Canadian Human Rights Commission has said last month's Federal Court ruling clears the way for First Nations to challenge federal funding for education, policing and health care.
The Justice Department filed notice Friday that it intends to challenge that ruling in the Federal Court of Appeal.
Jan O'Driscoll, spokesman for Aboriginal Affairs and Northern Development Canada, said that despite the decision to appeal, "we will, in the meantime, continue moving forward with willing partners to make progress with respect to child and family services."
He said the government has six framework agreements in place with the provinces and First Nations to fund child and family services.
He said that represent new annual investments of $100 million, bringing to $600 million the total invested in First Nations child and family services to 2012-13.
The ruling rejected the federal government's attempts to prevent First Nations groups from arguing for better funding for child welfare on reserves.
The ruling meant that First Nations and the federal government would have held a full-blown hearing about whether Ottawa is treating native children unfairly.
First Nations groups say Ottawa is discriminating against native kids because the support the feds provide for child welfare on reserves is much lower than what kids off reserves get from provincial governments.
Friday's appeal is the latest move by the federal government to block the case, arguing it is not fair to compare federal services to provincial services.
Note to readers: This is a corrected version. A previous story wrongly identified Aboriginal Affairs spokesman Jan O'Driscoll as a woman