Co-author Vandna Sinha, a professor at McGill University, says the problem persists despite the federal government's position that there are no violations of the so-called Jordan's principle.
"You get children and First Nations families caught in the middle," she said.
Jordan's principle holds that no aboriginal child should suffer denials, delays or disruptions of health services available to other children due to jurisdictional disputes. Jordan Anderson was a Cree boy from Norway House, Man., who died in hospital in 2005 after such disagreements kept him from spending his last years in home care.
"Just provide (the service), whether you're federal or provincial or whichever department, and sort it out afterwards," said David Morley, president of UNICEF Canada, which helped fund the study. "It seems that the bureaucratic mechanisms have been getting in the way of that simple, quick response."
As part of the study, 25 front-line workers in children's services were interviewed.
"All of them were able to point to differences in the process for accessing services for First Nations children and other children," Sinha said.
Statistics on the number of occurrences proved impossible to develop, she said.
"We'd have to go jurisdiction by jurisdiction, to each individual service provider, and ask them. Right now, nobody's even trying to count."
The report details stories of how First Nations children suffered while governments shuffled files.
Parents have been denied support even when their children require 24-hour care. An infant who wouldn't breastfeed and was allergic to normal formula couldn't get Health Canada to cover the non-allergenic type.
Federal and provincial governments dickered over the cost of a special crib for a baby with neurological disorders. A child with permanent hearing loss couldn't get a hearing aid because the province wouldn't pay for a service delivered on a reserve.
One band had to conduct community fundraising for a wheelchair for a paraplegic child because it felt it couldn't wait to go through Health Canada's three levels of review. Another band was in a three-year legal fight to get federal funding for a single mother to get help for her dependent son after she had a stroke.
"These jurisdictional disputes are getting in the way of children who are already so disadvantaged," said Morley. "These are already among some of the most disadvantaged children in the country."
A spokeswoman for Indian Affairs said the government has agreements to implement Jordan's principle with Manitoba, Saskatchewan, British Columbia and New Brunswick.
"There are currently no outstanding jurisdictional disputes involving Jordan’s principle in Canada," Emily Hillstrom said in an emailed statement.
Sinha said her research examined federal documents that show Ottawa defines the problem so narrowly it simply disappears.
The government, for example, doesn't consider disputes involving off-reserve aboriginals to come under Jordan's principle.
It doesn't consider disputes between departments within the same government, says the report. Nor does it include issues where a problem exists because of under-funding compared to non-aboriginal communities.
A case involving many of the examples raised in the report is currently in front of the Canadian Human Rights Tribunal. A ruling on it is expected in early April.
The report points out that in 2007, a motion endorsing Jordan’s principle was unanimously adopted by the House of Commons.