NHS trusts have faced rising numbers of flu cases and respiratory illness, with 48 flu-related deaths in England so far this winter.
The main strains circulating continue to be flu A(H3N2), known as Aussie flu, A(H1N1), known as swine flu, and flu B.
The Daily Telegraph reported that 10 Boots stores in the Midlands, east of England, South and South West had run out of the vaccine on Friday.
A spokeswoman for the firm said: "We've seen a very high level of demand in the recent week from people looking to protect themselves and their families against flu this winter and has meant some Boots stores temporarily ran out of stock for a limited time.
"We have quickly replenished our supply chain and flu vaccinations will be available (on Saturday)."
People aged under nine or over 65 can get a free flu jab, as well as people who are pregnant or have certain medical conditions,
A Department for Health and Social Care spokeswoman said: "Vaccines are the best protection we have against flu. As well as getting the jab from a pharmacy, patients can also book an appointment with their GP.
"We are in close contact with the vaccine manufacturers and we are confident there is sufficient vaccine availability."