The government agency said after flu shot clinics across the province close, some vaccine will be held back for children who need a second shot and for potential flu outbreaks at hospitals or continuing care homes.
The province estimates more than 1 million people in Alberta have been inoculated for the seasonal flu, including H1N1.
As of Wednesday, eight people in the province had died from this flu.
There were 1,571 confirmed cases in the province. Officials said 372 people have been hospitalized, including 54 in intensive care.
Alberta is trying to get more vaccine.
Health Minister Fred Horne said a national committee that reports to the federal government called the Vaccine Supply Working Group makes recommendations about how reserve stocks of flu vaccine should be distributed.
Horne said this committee is aware of Alberta's shortage.
"We have indicated that we expect our supply to run out by the end of the week," Horne said.
"We have certainly made it known that we would like more vaccine. We are not sure where that is in the process right now."
Dr. Frank Atherton, Nova Scotia's deputy chief medical officer of health, said Thursday that the province was willing to loan part of its reserve stock to any other province where there is greater need.
The Public Health Agency of Canada said it is up to the provinces to purchase what they need, but it has offered to help co-ordinate the sharing of vaccine doses.
"Seasonal flu numbers across Canada are normal, however certain jurisdictions are experiencing an increase in demand for immunization, in comparison to other years," Blossom Leung, a spokeswoman for the agency, said in an email Thursday from Ottawa.
"Public Health Agency of Canada has offered to help co-ordinate with the provinces and territories in securing and sharing additional vaccine."
Leung did not indicate whether vaccine from other provinces will be sent to Alberta.
Alberta Health Services said demand for the vaccine remains high, and the supply varies across the province.
In the meantime, the agency said that people should cover their mouth when they cough, wash their hands thoroughly and often, and stay home if they are sick.