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Bottles of flu vaccine rotate on a plate as they make their way through a GlaxoSmithKline assembly line on Dec. 9, 2004 in in Ste. Foy, Que. THE CANADIAN PRESS/Jacques Boissinot

The Canadian Press

Canada's largest flu vaccine supplier, won't be able to fill about 30 per cent of its Canadian order for the upcoming 2014-15 flu season, the company said Thursday.

It also suggested the problems at its production facility in Ste. Foy, Que., may have an impact on its ability to supply vaccine to the U.S. market from that plant this season.

GlaxoSmithKline, which now goes by the name GSK, said problems in this year's production run have left it with a shortfall of about two million doses. The company was slated to provide nearly 6.4 million doses, 53 per cent of Canada's total purchase of about 12 million doses.

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The Public Health Agency of Canada said it has secured 1.2 million additional doses of vaccine from other manufacturers which have a portion of the country's flu vaccine supply contract. Those companies are Sanofi Pasteur, Novartis and MedImmune, which is owned by AstraZeneca.

The Public Health Agency's statement, sent via email, suggested there may be delays in the delivery of the portion of the GSK contract that the company still believes it can fill.

"A new delivery schedule for the flu vaccine from GSK is still being determined but it is expected that deliveries will start in the second or third week of October, long before flu immunization demand reaches its peak," it said.

GSK said 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 said it identified irregular results in its routine quality control monitoring on Aug. 14 and suspended production to investigate and try to fix the problem. Production was reinstated on Aug. 26 but it will result in a delivery delay, the company said.

It also said it had "an invalid test result" on one component of the vaccine, which protects against three different strains of influenza.

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"Based on our standard, approved processes, retesting was required. The test results gathered to date ... are inconclusive. This will result in just under two million committed doses no longer available. We are continuing to investigate the cause of this issue," spokesperson Michelle Smolenaars Hunter said in an email.

Contingency planning had been underway in Canada since the Ste. Foy plant's problems were first flagged by the FDA in June.

The two million dose shortfall represents just under 17 per cent of Canada's total vaccine purchase for this year.

The news comes as provinces and territories are gearing up to start flu vaccination programs beginning next month.

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