Health officials say delays by the World Health Organisation (WHO) in selecting the vaccine for this winter mean that some jabs will not be delivered to GP practices until the end of November.
Normally flu vaccinations are offered by the NHS from September.
In a letter, seen by The Daily Telegraph, health officials urge GPs and pharmacists to check when their stocks will be delivered.
They said manufacturers have warned that the lateness of the WHO’s decision will mean some vaccine supplies arrive later than normal.
The WHO typically makes its recommendations about which strains of flu to protect against in February. But this year it delayed a decision on one strain - H3N2 - for a month, in a bid to adjust to mutations in the key strains in circulation.
Since then the virus has proved dominant in Australia, which is currently experiencing one of the worst flu seasons on record.
The country, which is now in the height of winter, has already had three times as many deaths as in the whole season last year, with around eight times as many laboratory confirmed cases as normal.
NHS officials hope that the jabs will arrive ahead of the UK’s flu season, which typically starts in December.
But this year Australia has experienced one of its earliest flu seasons in its history.
The delays to NHS jabs affect the “quadrivalent” jabs used for pregnant women and adults with health problems, such as asthma or diabetes.
Other types of vaccinations are offered to those aged 65 and over, using a boost designed to improve immune response, while children are given vaccination via nasal spray.
The letter from Mary Ramsay, head of immunisation at Public Health England, and Deborah Tomalin, director of public health commissioning and operations at NHS England, has been sent to all GPs and community pharmacists in England.
It says the WHO’s delayed recommendations - “in response to a recent increase in the proportion of viruses detected which would not be effectively dealt with by its existing vaccine strains” - are now set to have knock-on effects across the NHS.
“We understand from manufacturers that the delayed WHO recommendation on vaccine strain has had an impact on their vaccine supply.
Sanofi Pasteur have indicated they plan to phase some of the deliveries of the inactivated Quadrivalent influenza vaccines (QIV) for those at risk and under 65 years, with some vaccines being delivered by the end of November ahead of when the flu season usually starts.”
The drugs giant is one of four companies which will be isusing vaccines this year.
Alll GPs are now being urged to contact manufacturers to check when stocks will be delivered, in order to plan scheduling of appointments.
The disclosures come amid growing concern about how the NHS will cope this winter.
Last month 471 NHS patients waited for at least 12 hours on a trolley after arrival at Accident and Emergency departments. In June 2012 just two patients waited this long.