Many flu jab appointments will have to be rescheduled because of a two-week delay in the delivery of the vaccines to GPs.
Seqirus, the largest provider of flu vaccines to the UK, confirmed hold ups of as much as a fortnight in England and Wales, blaming "unforeseen challenges linked with road freight delays".
The firm sent a letter advising practices not to rebook appointments until a new delivery date is confirmed, GP online reported.
The correspondence did not explain whether the delays were related to the shortage of lorry drivers that has led to supermarkets running out of certain goods and some fast food outlets having to close.
Shadow health secretary Jonathan Ashworth said: "GPs are at their wits' end, first forced to cancel blood tests because of bottle shortages and now we learn flu vaccines will be delayed.
"This has been a summer of crisis for the NHS with patients paying the price."
He said ministers "must urgently get a grip" given the risk posed by the flu in the coming months.
A Seqirus spokesperson said the company is "working hard to resolve the delay to allow customers to reschedule their influenza vaccination clinics".
Dr Richard Vautrey, British Medical Association GP committee chairman, said the issue will probably affect a "significant proportion" of practices.
He said: "Many practices will have spent the last few days and weeks meticulously planning for their flu vaccination programme, inviting and booking patients in for their jabs, only now to have to contact them all again to cancel or reschedule appointments.
"This causes a huge increase in staff's already unsustainable workloads, and inconvenience and unneeded anxiety for patients who will be keen to be protected ahead of winter."
He said it is "incredibly concerning" that the delay appears to be stemming from issues around freight transportation, not unlike the shortage of blood test bottles reported last month.
"We must ask the government exactly what it is doing to urgently address this," he added.
The seasonal flu programme in England began this month, with the health secretary touting it as the biggest in the country's history.
Sajid Javid urged everyone eligible to get the vaccine, which will be made available to more than 35 million people for free.
For the first time, those eligible will include all secondary school pupils up to Year 11 - children aged 15 and 16.
The target for 2021 is almost double the amount of jabs that were administered last winter amid concerns about the combined impact of flu and COVID-19 this winter.