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The capital is at risk of having about 70,000 fewer doses than it needs, Shadow Health Secretary and London MP Wes Streeting told the Evening Standard.
He said the problem was most acute in North East London and walk-in appointments were being curtailed in Redbridge.
Problems are also being reported in South East London, where officials were scrambling to check on supplies.
But health sources said on Friday night that action had been taken after the alarm was raised several days ago and there was confidence that all Londoners seeking a jab would be able to get one. Deliveries were being made this afternoon.
The capital’s health chiefs were hoping to deliver a record number of boosters this weekend as people rushed to get protected from the Omicron variant before Christmas.
Thousands of people are already booked in to mass vaccination clinics being opened at Chelsea’s Stamford Bridge stadium on Saturday, Wembley Stadium on Sunday and Charlton FC’s Valley ground on both days.
In addition, the Business Design Centre in Islington is reopening on Saturday morning as a vaccination centre and will offer first, second and booster Moderna jabs, Islington council announced.
About 100,000 jabs a day are currently being given in the capital in a “race against time” as Omicron became dominant.
Mr Streeting, MP for Ilford North, said: “It’s deeply concerning that London is being hit by a vaccine supply shortage when we are also the region that has the Omicron surge.
“It’s inexplicable that the Government have had days’ notice to deal with this and have not done so and that now walk-in appointments at GP surgeries, pharmacies and pop-ups are being cancelled.”
It is understood there is no national shortage of vaccines but there has been a problem distributing supplies a number of the new vaccination hubs.
Issues were first flagged with national health chiefs on Tuesday – with a request for military assistance - but remain unresolved.
One source said: “The scale of [the shortages] looks quite significant. Everyone is battening down the hatches.
“We have been spending the whole week signing everyone up for a huge vaccine push this weekend.
“There is a lot of concern in the system that, after a week’s worth of hard work, we are not able to have the number of vaccines we need in order to vaccinate Londoners.”
On Friday afternoon, the Standard was told that efforts were underway to get more jabs to north east London and that “no-one who wants a jab will not be able to get one”.
Redbridge council said it was “aware of the system-wide pressure across London” and was working to resolve issues, but still planned to open walk-in centres in Woodford, Ilford and Barkingside this weekend.
Will Huxter, director of NHS London’s Covid vaccination programme said: “We are seeing record numbers of Covid vaccinations across the capital and our focus is on ensuring these vaccines get to people as quickly as possible so they can get the vital protection they need against the virus.
“This weekend, vaccines are available at hundreds of pharmacy and GP sites, hospitals and vaccination centres – as well as at pop-up events at major venues including Wembley football stadium, so please do book in at a site near you.”