The British Medical Association (BMA) said it is "grossly unfair" to reschedule the appointments of patients due their second dose of the Pfizer Covid-19 vaccine in favour of people seeking their first dose.
Initially it was advised that people should receive their second dose around three weeks after getting the first jab, but the advice has been changed to 12 weeks.
On Wednesday the government changed its guidance so it could vaccinate more people with the first dose of jab as studies shows it provides some protection against the virus.
Dr Richard Vautrey, chairman of the BMA GP committee, said GPs were concerned at the change of guidance.
He said: "It is grossly and patently unfair to tens of thousands of our most at-risk patients to now try to reschedule their appointments.
"Local leaders are telling us that is unprofessional and impractical to amend the appointments for thousands of frail elderly patients, particularly those booked and who have already made arrangements to have their second vaccination in the next two weeks.
"The decision to ask GPs, at such short notice, to rebook patients for three months hence will also cause huge logistical problems for almost all vaccination sites and practices.
"For example, to make contact with even just two thousand elderly or vulnerable patients will take a team of five staff at a practice about a week, and that's simply untenable.
"The BMA believes the existing commitment made to these patients by the NHS and local clinicians should be respected. If GPs decide to honour these booked appointments in January, the BMA will support them.
The decision to ask GPs, at such short notice, to rebook patients for three months hence will also cause huge logistical problems for almost all vaccination sites and practices
"The government must see that it's only right that existing bookings for the oldest and most vulnerable members of our society are honoured, and it must also as soon as possible publish a scientifically-validated justification for its new approach."
Following the approval of the Oxford vaccine, defence secretary Ben Wallace said up to 250 teams of combat medics could be made available to help deliver the Covid-19 vaccine rollout across the country.
Speaking to Times Radio, Mr Wallace said: "We’ve already put 133 (army medics) into the overall vaccine taskforce but I’ve also got plans for up to 250 teams of mobile, medically-trained personnel who could go out and administer the vaccine around the country.
“That would be over 100,000 a day they could potentially deliver if that is requested by the NHS – and we are planning to grow that if possible.”