The N.W.T. department of health is now limiting flu shots to people at high risk of developing serious illness from influenza, giving priority to women who are pregnant and to children under the age of five.
The department made the announcement Friday morning.
There have been 53 confirmed cases of flu in the territory so far this season, all H1N1. Thirteen people have been hospitalized, one in the Intensive Care Unit. No one has died.
Officials say a surge in demand for the flu vaccine led to the current shortage.
The N.W.T. initially ordered 15,250 doses of flu vaccine at the beginning of the season — enough for about 36 per cent of the population
Last week, the territory had 3,000 doses of flu vaccine left. That supply has now dropped to about 700.
Dr. Andre Corriveau, the N.W.T.'s chief public health officer, says 35 per cent of the territory's population has now been vaccinated against the flu, the most in four years.
The department says it is working with other jurisdictions to get more vaccine.
Another 590 vaccine doses are expected to arrive next week. These were ordered before officials knew they were running out.
The department is hoping to acquire 1,500 more doses this month from outside Canada.
Saskatchewan has also begun restricting flu shots to high risk groups.