"This is a concern, and we are investigating," Health Minister Leona Aglukkaq told a press conference.
"Since the outbreak of H1N1 began, our government has been working to ensure accurate and timely information gets to First Nations communities," she said.
Additional health staff and protective garments have been sent to several native communities to review situations and determine how the virus reached the remote centers.
Canadian health officials, however, could not quantify the number of natives infected with the virus, and downplayed fears.
This week, World Health Organization acting assistant director-general Keiji Fukuda raised concerns over "a disproportionate number of serious cases" occurring in Canada's aboriginal communities.
He said there were "a larger number than expected" cases of young natives who had developed a "serious illness" and "had to get hospitalized."
Canada's public health officer David Butler-Jones, however, said that it was "much too early" to conclude "based on a couple of communities that this is somehow a disease that is worse among one ethnic group.
"This is not an indigenous disease," he said. "We know there are certain risk conditions, underlying chronic disease, etcetera, that make (some) at greater risk of disease or death."
However the A(H1N1) virus "is a disease that affects everybody and we don't yet have the data to understand why some communities" may be hit harder, he said.
Native leaders this week accused Canadian health officials of ignoring their plight.
"It has taken way too long to recognize how bad the situation is," David Harper, chief of the Garden Hill First Nation in Manitoba province, told the Globe and Mail newspaper.
At least half of some two-dozen serious cases in Manitoba are reportedly aboriginals, including three children and two pregnant women.
Several of the patients with serious cases were flown from northern wilds to hospitals in the provincial capital Winnipeg, and put on ventilators.
Some natives fear a repeat of the 1918 Spanish Flu pandemic, the last time an influenza virus hit Canadian natives hard, wiping out entire villages in some cases.
Canada updated its nationwide swine flu count on Wednesday to 2,978 confirmed cases, including 533 that required hospitalization. Four people have already died of the disease.
Canada currently has the third-largest number of swine flu cases in the world, behind the United States and Mexico.
Officials noted a spike in the number of cases in Canada over the past month, but said they remain optimistic the spread of the disease would slow over the summer.
"Thankfully here in Canada, the vast majority of illnesses to date remain mild," Aglukkaq said, adding Canada was moving forward on the development of a vaccine.
Earlier, the World Health Organization raised its pandemic alert level to phase six, declaring the first influenza pandemic in four decades.
"This decision does not change our approach here in Canada," Aglukkaq said.