Canada's top doctor says health officials didn't expect so many people to line up for the swine flu shot.

Dr. David Butler-Jones, the chief public health officer, told a national news network that as recently as three weeks ago officials didn't foresee the long lineups that have choked clinics giving out the H1N1 flu vaccine.

"Three or four weeks ago, what we could not anticipate was the number of people that are interested," he said.

Thousands of Canadians have been vaccinated since Health Minister Leona Aglukkaq approved the H1N1 vaccine in late October - after other countries had already begun vaccinations.

But there have been long lineups, confusion and frustration across the country as people rush to get the vaccine and some are turned away.

The swelling crowds at vaccination clinics are in stark contrast with earlier polls that showed few Canadians planned to get the swine-flu shot.

But that was before the recent deaths of three Ontario children who caught H1N1 - with another death still unconfirmed - put a human face on the virus and galvanized worried Canadians to get themselves and their families vaccinated.

Clinics are also coping with a shortage of vaccine from manufacturer GlaxoSmithKline. The drugmaker will only be able to produce about 400,000 doses of the vaccine this week instead of the million or so doses that officials expected.

The shortage stems from production problems that arose when GlaxoSmithKline switched from making the adjuvanted version of the vaccine - which contains a booster compound - to making special unadjuvanted batches for pregnant women and young children.

A government source told The Canadian Press that GlaxoSmithKline had forewarned Ottawa that the switch to making the unadjuvanted vaccine would slow production. But the vaccine maker apparently underestimated how much the changeover would choke supply.

So instead of the 1.3 to 1.5 million doses that GlaxoSmithKline had anticipated, the drugmaker can now only supply some 436,000 doses for the coming week.

"GSK overstated their amounts," Aglukkaq told a national news network.

"They will continue to produce the vaccine. But we will continue to work with them as we roll out the vaccine."

Butler-Jones has said the federal government didn't know the extent of the shortfall until last Thursday. But he said production is expected to ramp up again the week of Nov. 9 and health officials don't expect any more hiccups.

He also defended the rollout of the vaccine.

"If a year ago we knew exactly what the virus was, what the pandemic was going to be, then the production of vaccine could have taken place," Butler-Jones told the news network.

"But we're actually living in real time. We're producing vaccine while we're testing it, while we're distributing it and while we're giving it."

Butler-Jones again asked Canadians who are at lower risk if they catch the flu to hold off on getting the H1N1 vaccine until the most vulnerable people are vaccinated.

Those deemed to be at high risk are pregnant women, children over six months but under five years of age, health-care workers, caregivers for those who are vulnerable and unable to get the vaccine, people under 65 with pre-existing health conditions, and those who live in remote or isolated communities.