GP surgeries across Britain were forced to turn away vulnerable people this week due to the shortages, while the flu death toll rose to 50 since the start of October.
Leftovers from last year's swine flu vaccine - which does not offer protection against all the different flu strains - are being used to cover the shortfalls of this year's vaccination programme.
Mr Cameron, who revealed he had not been immunised this year, disputed suggestions that the shortfall had been caused by spending cuts. He insisted that the Government had followed expert advice throughout the vaccination process.
Speaking to BBC Radio 5 Live, he said: "Doctors did order something like 14 million doses of vaccine. Because of very heavy usage there are some shortages in some places.
"It is very important that we learn the lessons from this.
"One of the lessons is that it looks likely that, because of the prevalence of swine flu and other strains, we might have quite significant outbreaks in future years and we need to look at the way we order vaccinations and whether more needs to be done.
"We have followed at every turn what the joint committee (on vaccinations and immunisations) has said. It is important you listen to the experts and make sure you are trying to get the vaccine to the people who need it."
He added: "This is nothing to do with cuts. The NHS is not having cuts."
A Department of Health spokeswoman said: "The Department of Health each year routinely assesses performance over the flu season in order to provide the NHS with the best possible guidance for the following season.
"We have already said that we are reviewing specifically the need for central procurement of vaccines. This review will report in due course."
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