People who are not in an at-risk group should be banned from having private flu vaccinations, the chairman of the Royal College of GPs has said.
Dr Clare Gerada told the Daily Telegraph allowing healthy people to buy the flu jab had compounded NHS shortages and left others vulnerable.
There are reports some GPs in England have run out of stock.
The Department of Health said it could not prevent pharmacies from selling the vaccine commercially.
Nearly 15 million doses of seasonal flu vaccine have been delivered to the UK.
Usually that is more than enough but this year there has been a late surge in demand, with reports that some people most at risk from flu – including pregnant women and those with underlying health problems – have been unable to get the vaccine.
Some pharmacies have offered the jab privately for about £15.
Dr Gerada told the newspaper the private flu vaccinations had affected the “delicate balance” of availability and should be stopped by the government.
She called for a study looking at how many healthy people had paid to have the jab privately, to gauge “whether there should be a law that they are not allowed to have it”.
A spokesman for the Department of Health told the paper: “Community pharmacies are working with GPs to ensure that at-risk groups are vaccinated, as far as is possible, with limited remaining stock.
“Pharmacies are private businesses and we are not able to prevent them from selling the vaccine commercially.”
Last week the government announced that old vaccines left over from the 2009 swine flu pandemic would be used to plug the shortfall in this winter’s supplies.
The 2009 vaccine is different from the jab being offered this year.
It offers protection against just one of the three strains, but as swine flu is the dominant strain in circulation the government said it was the best option available.
Labour has accused the government of being slow to act, but on Monday Health Secretary Andrew Lansley said the NHS was “well prepared and responded excellently” to the seasonal flu outbreak.
GPs in England and Wales – who order vaccines directly from manufacturers – have also faced criticism for not ordering enough of the seasonal flu vaccine to protect all those in the at-risk groups.
They base these on the number of people who come forward for vaccination in previous years.
The number of deaths this winter from flu verified by the Health Protection Agency currently is 50, with 45 of these due to swine flu.
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