The Nutrition North Canada program comes into full effect today.
The program was rolled out slowly to make for a smooth transition from the old food mail program.
As of today, many non-perishable items like canned soups, canned vegetables and dry rice and pasta are no longer subsidized.
Retailers have been preparing for today's deadline for months, so prices won't jump instantly.
The North West Company owns and operates many grocery stores in Nunavut and the N.W.T. It has already secured an extra two months' supply of those non-perishables by sealift to Nunavut.
Michael McMullen, the company’s vice president of northern retail, said the company has also cut down on the number of brands it carries to make room for the larger sealift order instead of building a new warehouse.
"We would rather be more efficient with the resources we have available than invest money needlessly and be in a position of having to pass on those costs of construction to the customer," said McMullen.
McMullen said if prices do increase, it wouldn't be until late spring or early summer.
"It's not October 1 so much that we worry about. It's more as the sealift supply dwindles, it's more did we gauge the customer demand correctly."
Shoppers will have to wait until mid-2013 to see any potential impact on prices.
Program representatives say that since the new program started, the price of a northern food basket dropped by eight per cent. However, opinion among shoppers varies as to whether there have been more savings as a result of the program.