Doctors working in large practices have had to delay the swine-flu vaccination programme because of a flawed distribution strategy, medical website Pulse says.
The Department of Health (DH) has already or will soon deliver the first shipment of 500 doses to each surgery in the country, but larger health centres say they are already running low.
"We're irritated that small practices received the same number of vials as large practices," Dr Toby Davies, a GP in Tidworth, Wiltshire, told Pulse.
"We cannot order any more until 16 November and are told that deliveries will take one to two weeks from that date. The plan was to give 500 vaccines every Saturday morning, but clearly after this coming week we will run out and can't do any more until the end of the month."
Responding to the allegations, a DH spokesman said the current plan was "fair", but added supplies would be distributed differently in the future.
"The only fair way to get the limited stock we have to every surgery quickly was to send one box of vaccine to every GP," he said.
"GPs should talk to their PCT to discuss arrangements so that, when we have more supplies, they can be distributed proportionally."