the upcoming 2014-15 flu season.
GlaxoSmithKline, which now goes by the name GSK, says problems at its production facility in Ste. Foy, Que., have left it with a shortfall about two million doses.
The company was to supply 53 per cent of the vaccine ordered by the provincial, territorial and federal governments this year.
GSK says in an email that the production problem was unrelated to the concerns raised earlier this year in inspections by the U.S. Food and Drug Administration and Health Canada.
The FDA had issued a warning letter after it found a variety of problems in its inspection, a number stemming from bacterial contamination in the plant's water supply.
The company's email does not detail what new problem had led to the vaccine shortfall.
"We are continuing to investigate the cause of this issue," spokesperson Michelle Smolenaars Hunter says in the email.
"We have informed Health Canada and are also providing regular updates to them, as well as PHAC" — the Public Health Agency of Canada.
Contingency planning has been underway in Canada since the Ste. Foy plant's problems were first flagged by the FDA in June.
Other licensed manufacturers have been asked if they could provide additional doses for the Canadian market, though it is unclear if there is enough excess in the system to cover the full two million dose shortfall.
That shortage represents just under 17 per cent of Canada's total vaccine purchase for this year.
Sanofi Pasteur, Novartis and MedImmune also provide portions of the Canadian purchase, which is bulk bought by Public Works and Government Services Canada.
The news comes as provinces and territories are gearing up to start flu vaccination programs beginning next month.
Smolenaars Hunter could not immediately answer questions about whether the production problem would also affect deliveries to the United States. The Ste. Foy plant is supposed to provide 23 million doses of vaccine to the U.S. market this fall.