Flood-hit areas could see vaccine doses diverted away, Government sources say amid fears towns and villages could become cut off.
Severe flood warnings are in place across swathes of the North West, with hundreds of residents told to leave their homes overnight because of adverse weather caused by Storm Christoph.
A Whitehall source said that in the short-term, supplies will be held back for any vaccination centres which have to close because of flooding, in order to catch up with missed jabs as soon as possible.
But he said that if flooding meant clinics were forced to close for several days, supplies would have to be diverted to parts of the country which could use them more quickly.
Over 160 flood warnings remained in place across England on Thursday, with three "severe" warnings - meaning danger to life - issued for parts of the North West.
The source said: “There is a great deal of concern about the impact of flooding across the north of England. “If we see severe flooding some of the vaccination centres will have to close, and people will be told to rebook, in those situations. If it lasts a couple of days, it will just mean a delay, but if it goes on longer than that we would look to divert supplies, because we do want to make sure all the supplies get used as quickly as possible.”
The situation raises the prospect that victims of the storm could be put at increased risk of covid, because of difficulties accessing vaccines.
It also comes amid concern about a postcode lottery in provision of jabs across the country, with those living in London far less likely than those in the North and Midlands to have been offered the vaccine.
Supplies of vaccines to GPs in the North East and Yorkshire region will be halved next week, because the region is ahead of other areas, Health Service Journal has reported.
NHS sources said there are no current plans to close vaccination centres, but said the situation would be kept under review with the weather.
On Thursday the prime minister visited Didsbury, one of the worst flood affected areas, a day after he held the second Cobra meeting in two days over the extreme weather.
The Government is concerned about the logistics of dealing with a double crisis as the pandemic complicated the flood response.
The prime minister was criticised last year for being too slow to call a Cobra meeting and visit communities after major floods hit the Midlands, Wales and parts of Yorkshire.
"There will be more to come, there will be further rain next week, so it is vital that people who are in potentially affected areas follow the advice and get the Environment Agency flood alerts where they can,” he said.
Families were encouraged to stay with friends and family, rather than crowd into evacuation centres set up in flooding hotspots, in order to reduce the Covid risk.
The Government said travel and household mixing restrictions would not apply to any of those evacuating from flood-hit areas.
Hundreds of people evacuated from the Warrington area, which was last night under further flood warnings from the River Bollin.
Kathryn Buckley, a councillor in Lymm, on the River Bollin, said the pandemic meant dealing with flood logistics was a “massive struggle”.
“The Covid situation has made things far worse,” she said.
Authorities attempted to find hotel spaces for anyone who was self-isolating or vulnerable, while Covid measures were implemented in other evacuation centres.
The government has encouraged people to keep their vaccination appointments as much as possible, but is also concerned about extra pressure on the NHS from any flood-related incidents.
Three severe flood warnings remained in place last night for the River Dee at Farndon, and the River Bollin at Little Bollington and Heatley in Warrington.
While a brief respite is expected from the rain, water levels are already so high that the rivers could continue to rise and possibly breach defences.
Gabrielle Burns-Smith, 44, whose home in Lymm flooded, said that she "watched the water coming through the back door" in the early hours of Thursday morning.
She said: "By 3pm yesterday the water outside was shin-deep and by 4pm it was knee-deep, and we were seriously worrying that the house was going to be breached. Then it was.
"We're still in the house, we can't go anywhere because we can't get the car out, the water is just too deep. Both our living rooms are flooded."
Homes were flooded following heavy rainfall and snow showers in Cheshire, with roads disrupted and residents in the county warned that river levels were still rising on Thursday.
In Northwich, Cheshire, elderly residents from two care homes were evacuated by fire crews with dinghies on Thursday afternoon.
Residents in Bangor-on-Dee, Ruthin, north Wales, and Maghull, Merseyside, were also encouraged to evacuate. Bangor-on-Dee council clerk Sean Merry said the River Dee was the “highest I’ve known in 25 years”.
Police said the body of a man had been recovered from the River Taff near Blackweir in Cardiff on Thursday, with the death being treated as unexplained.