Sir Malcolm Grant, chairman of NHS England, last night said he fears hospitals will be "inundated" with cases, despite attempts to bolster services.
His warnings came as the country’s Chief Medical Officer told the Daily Telegraph that she fears the jab may not protect the elderly this winter, but said it is still “our best hope” to stave off an NHS crisis.
Dame Sally, England’s most senior doctor today urged 21 million people eligible for free vaccinations - including young children, pensioners, and health workers - to take up the jabs.
However, last year’s jab had zero effectiveness among over 65s, an official evaluation reveals, while protecting two in three children.
This year’s programme will push further on trying to protect those who come into contact with pensioners, in case the vaccination fails as badly this year, with fears flu rates could be far higher.
In a letter sent to all NHS workers, staff are told to “do their duty” and get vaccinated - with those who opt out told they will have to explain themselves.
More than one million care home workers will also be offered the jab, in a bid to reduce levels of transmission to vulnerable residents.
It comes amid fears “precarious” NHS services could be overwhelmed by a heavy flu season.
Health officials are anxious about how hospitals will cope if patterns seen in Australia - which has just battled the worst flu season for almost two decades - are replicated here.
Yesterday Sir Malcolm Grant, chairman of NHS England, said health service leaders were extremely fearful of what this winter could bring.
He told a conference in Bournemouth: “We face winter better prepared than we have ever been, but more scared than we have ever been.
“We have the strong likelihood of hospitals being inundated with people suffering flu.”
Officials are particularly fearful because of evidence that last year’s vaccine failed to protect those over 65.
An evaluation of last year’s programme, seen by The Daily Telegraph, shows pensioners who had the jab fared no better than those who did not. Protection rates were far higher among children, with 66 per cent protection, the figures show.
This year’s vaccine is similar to last year’s, which failed to effectively counter strains like those which have recently proved virulent in Australia.
As well as focussing on children, who are “super-spreaders” of the vaccine, officials hope heavy vaccination of NHS and care staff who come into contact with the elderly will help to reduce the risk of transmission.
Prof Dame Sally urged all those eligible for the jab to take up the offer, saying it was the best protection on offer.
“At this stage in the winter none of us know how it is going to go,” she told The Telegraph.
“It wasn’t very effective last year but it is our best hope. I’ve had mine,” said Dame Sally, 67.
A letter from the chief medical officer and other medics has been sent to all staff, telling them that it is their“duty” to protect patients and colleagues by having the jab.
From this year, 1.4 million NHS employees will be told that it is the “default” position to be vaccinated, and that full records must be kept explaining why any staff opt out.
Health officials hope the move will “nudge” tens of thousands of staff into having the jab, and stop them neglecting to do so just because they forget, with just one in five employees being vaccinated at some trusts.
The letter says healthcare workers should undergo vaccination in order to protect those in their care - with one in three flu cases passed on by those without any symptoms.
“As winter approaches it is worth reminding ourselves that flu can have serious and even fatal consequences,” the letter warns.
It comes as new figures show that latest A&E performance for September is the worst on record for the month, with 89.7 per cent of patients seen in four hours. The statistics also show a 63 per cent rise in numbers waiting at least a year for treatment, over the last 12 months.
Health officials have repeatedly urged hospitals to empty thousands of beds, amid fears that levels of bed occupancy are too high to cope with spikes in demand.
Earlier this week, the chief executive of NHS England suggested the NHS needed extra funds, saying it would be “very hard” for the service to do what is asked of it without more money from next month’s budget.
Ministers have just written to the worst performing councils, threatening to cut future funding if if they do not cut levels of bedblocking.
Yesterday health officials issued details of winter plans, including the creation of a new national emergency pressure panel to track risk levels and warn national leaders of impending crisis.
They also launched a four year plan to increase staffing in A&E departments in the long-term.
As well as an expansion in consultants - with an extra 100 trained each year, including some brought here from India and Pakistan, the NHS will attempt to recruit around 1,000 assistants, to work alongside medics.