There are fears that vulnerable people could have to wait for their flu jab after the Government confirmed stocks would arrive late.
The jab is usually given to high-risk groups first, including the over-65s, people with respiratory conditions like asthma, and those with chronic conditions like diabetes.
Earlier this year, manufacturers were forced to switch to growing a flu strain for the vaccine called 161B after another strain, Wisconsin 161, failed to grow. That has resulted in delayed deliveries to GP surgeries.
The Department of Health says the situation was better than it predicted in June but warned that some surgeries in England would have to share their stocks. The Department has ordered 15.2 million doses for across the UK - around a million more than last year. It said there should be enough doses in the long-term but some patients would have to wait.
A shortage last year led to a row after the Government claimed GPs were giving flu jabs to the "worried well", instead of prioritising at-risk groups. By the end of this October, GP surgeries will have received more than 9m doses, and a total of 13m doses by the end of November. The full delivery of 15.2m doses should be completed by the end of December, the Department of Health said.
Those figures compare to last year's when 2m doses were delivered by the end of September and 10.5m by the end of October.
Dr David Salisbury, director of immunisation at the Department of Health, said GPs would have to match supply and demand. They would be helped by local flu co-ordinators to "iron out feast and famine" at a local level, he said. "Practices that were late putting in their orders are not going to be at the front end of the queue in getting their deliveries.
"We want them to be sure that they are using their vaccine wisely so that people who have got clear risk factors are the ones they are bringing in according to a priority list we sent out earlier this year."
Dr Salisbury said the Government could not give assurances that everybody who needed a vaccine would get one in October. He recommended that patients call up their surgery and ask about availability. "Some people will have to wait but there will be a vaccine for them," he added.
There are fears that an early flu season could leave thousands without protection from the annual jab. "That's a situation that we face every single year," Dr Salisbury said. "It's not predictable as to when the influenza season will be."
