Some practices have had to turn away vulnerable people this week as the death toll from the virus continued to rise. Recent figures showed the number of deaths from flu since the start of October was up to 50.
Professor David Salisbury, director of immunisation at the Department of Health, said: "We have a large stock of vaccine.
"We have now got online ordering so that GPs will be able, from Monday, to simply order online from us and we will get deliveries very quickly, of large doses, large stocks of vaccine to them."
Prof Salisbury said that, although the number of people reported to have the flu virus appears to be settling, last week was not a "full reporting week", so doctors were only running their surgeries for three out of five working days.
He said: "We're having to make some assumptions about where this may be going. I think it's really difficult to call. It could flatten, but we could also see the numbers begin to edge up again next week."
The Government has been accused of not ordering enough doses of the vaccine for this year's flu season, but Prof Salisbury said the same amount was ordered last year and the year before.
He said: "It should indeed be sufficient for those people who are in risk groups - the ones who we really want to vaccinate. "I suspect that healthy people have indeed been asking. It is very hard to be able to work out why the right number of doses have not gone far enough when the number of people in risk groups, so far, have not exceeded the numbers vaccinated in previous years."
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