Doctors are reportedly being forced to throw away vaccines rather than administer second doses or use them on staff.
The revelation comes as hospitals become increasingly overwhelmed by the surge of COVID patients as the virus continues to spread across the UK.
GPs setting up vaccine clinics at short notice who find they have several injection doses left have reportedly been warned by local authorities that they cannot use them on staff or any patients who have already received their first jab.
Medics claim the policy, which has been described as “bordering on criminal”, is hampering the effort to vaccinate over-80s, along with frontline health and care workers.
The instructions are being reported across the country, according to The Telegraph.
Dr Robert Morely, director of professional support at the Birmingham Local Medical Committee, told the publication that the orders are "extremely counterproductive, nonsensical and ludicrous".
He said: “This is ridiculous, bordering on the criminal, to actually be wasting vaccines when you have the worst global healthcare crisis for a century."
Dr Morley said that GPs are struggling to book the exact number of appointments per vaccine due to the uncertainty of the supply chain. He added that some patients do not turn up after booking at short notice.
Instead of throwing away the leftover doses, Morley said: “The logical thing to do would be to use it as a second dose for healthcare workers, for example, who may be there in the building.”
NHS England reportedly sent out a letter to GPs on Monday telling clinics that no one should be given a second dose but Morley says he believes this “strong decree” is being taken too literally by local health officials.
Morley said some doctors are taking a stand against the policy and are being “very robust” in deciding to give the second dose.
Watch: COVID-19: Disruption to vaccine rollout as people trek for miles in snow
But he added that others “feel less secure and more threatened” with fears their vaccine supplies will be cancelled at short notice, their funding will be withheld or their GP contracts could be put at risk.
It comes as healthcare workers continue to administer the Pfizer/BioNTech vaccine, which makes up a large amount of the UK’s current vaccine supply. Batches only last a few days after being defrosted so they must be used quickly or they go to waste.
Dr Brian McGregor, a GP who chairs the BMA's Yorkshire regional committee, told the Telegraph that NHS England ordered his local clinical commissioning group to throw away any unused doses.
McGregor claimed they had been warned they would be "performance managed" on the issue.
"They control our contracts, payments, vaccine supply, regulation, and can make life unbearable," the doctor added.
Dr Julia Patterson, founder of Every Doctor, a campaign to protect the NHS and its workers, echoed the claims saying at least six different workplaces had told her organisation doctors had been forced to bin leftover doses.
The BMA's chair of council, Dr Chaand Nagpaul, told the newspaper: "Reports of vaccination sites feeling pressured to discard unused doses of the Pfizer vaccine are extremely concerning.
“This is absolutely unacceptable and morally wrong. Any wasted dose denies a real person the chance to be protected from serious illness or even death.”
He said: "NHS England needs to urgently clarify that doctors and staff have the discretion to ensure that they can make full use of any unused vaccines, rather than have any go to waste. "
An NHS spokesman has told media outlets: "There is absolutely no reason why vaccines should be wasted.
"Local vaccination sites should be managing their appointment lists to ensure all appointments are filled and they have a back-up list of patients and staff who can receive the vaccine at short notice."
Yahoo News has contacted NHS England for comment.
UK: Coronavirus vaccine centre opens in historic cathedral