The Native Women's Association of Canada says all of its funding from Health Canada is being cut, which makes up about 20 per cent of the organization's total budget.
Claudette Dumont Smith, executive director of the association, said she was "very surprised" by the funding cut.
"The amount is not extraordinary — less than a million. We do a tremendous amount of work," said Dumont Smith, executive director of the association.
"It's a drop in the pond, so to speak, on federal moneys. It is surprising that they would choose to cut the Native Women's Association of Canada. It is surprising when we are trying to improve the health of aboriginal women who are in fact the least healthy of all Canadians."
The association has offices across the country including the Northwest Territories and Yukon.
Without that money, the association said it will no longer be able to offer its HIV awareness or diabetes prevention programs and will cut four jobs.
Health Canada stated in an email, "The priority is to protect front-line health services for First Nations and Inuit communities. As this organization does not deliver health care services to communities, no direct services will be affected."
The association said Health Canada is focusing on services for First Nations living on reserve, while 70 per cent of aboriginal women live in rural and urban centres.