Dr Matt Curtis, a GP in West Yorkshire, says he and his team often only get three days to plan, staff and book a rota between being told about a delivery of vaccine and the supply arriving.
A large proportion of vaccines across the region are being administered by family doctors, though larger vaccine hubs and community pharmacies are now helping the effort to get the top four priority groups vaccinated by February 15.
But there have been contradictory claims about how the vaccines are being distributed to different regions and whether supplies have slowed to Yorkshire - which has rolled out its programme very quickly - to allow other areas to catch up.
Dr Curtis, Medical Director for the AWC Modality GP super-partnership, said poor communication from the centre to local areas had been frustrating.
He told The Yorkshire Post: "The way that this has been explained to us could have been better. We need to have openness and transparency.
"If our government were able to say 'yes, this area is going to get more because there's more people who need vaccinating there', you might not agree with that approach but at least it is honest."
Another difficulty is the short time-scales GPs have to work with, as vaccination clinics cannot be planned and patients booked in until practices are told how much they are getting and when.
Dr Curtis said: "I don't know how many vaccines I'm going to get and I don't know what day they're going to arrive.
"I fear that this heightens the inequality in the system in that if you've got a car or a family member who is able to take you, at short notice you can be taken to a vaccination appointment.
"Whereas if you don't have a phone or struggle to answer it and you don't have those transport links, it's much harder for you to be invited or to accept the invitation.
"So our worry is that the people who are perhaps most vulnerable are missing out on the vaccines by virtue of the very short notice.
"We are very fortunate that the Bradford District and Craven Clinical Commissioning Group have made huge efforts to get clarifications from NHS England when needed and it has supported us every step of the way."
Dr Curtis said the number of over-80s in need of a vaccine varies across his patch, with Craven having more such patients than Keighley because of its healthier population.
And he said: "We understand that it would not be equitable to give each practice the same number of vaccines regardless of their population. Some practice groups will need more and some will be able to deliver them faster than others.
"My feeling is that parts of the country where there are higher levels of people over 80 who have still not received the first vaccination are rightly receiving more vaccines now so that they can catch up."