Whitehorse and Yellowknife are expecting to be re-stocked with flu vaccine after supplies dwindled last week.
Last week, as the supply of vaccine ran low, the N.W.T. began restricting flu shots, giving priority to high risk individuals.
Yukon completely ran out of vaccine last Friday.
Despite the shortfall, Dr. Brendan Hanley, Yukon's chief medical officer of health, said Whitehorse is relatively well protected from the flu.
"It's a fairly intense flu season here; we have lots of people affected," he said. "On the other hand, we're seeing lots of people immunized, and we do know that there's at least some degree of protection from people who have been previously immunized."
Hanley said remaining vaccine in Canada will be pooled and redistributed this week. He expects Whitehorse will receive a few hundred doses, enough to run another flu shot clinic. The time and location of the clinic won't announced until the vaccine is in the territory.
The N.W.T. expects to receive 600 more doses of flu vaccine on Wednesday. N.W.T. health officials say they will continue to give priority to vaccinating children under the age of five and women who are pregnant.
As of Monday, there were 69 confirmed cases of H1N1 flu in the Northwest Territories.
Nunavut Health officials say they have enough flu vaccine to meet demand, despite the shortages elsewhere.
Nunavut's health department is now offering the FluMist vaccine to anyone between the ages of two and 59 until Jan. 20. FluMist is sprayed in the nose instead of being injected in the arm.
The vaccination is available free at the territory's health centres.