MMR and flu injections traditionally given at local doctors' surgeries are to become the responsibility of clinics set up by health boards.
The move is designed to reduce the workload of GPs.
But some doctors argue that in rural areas people might miss visits due to longer journeys to attend the clinics.
NHS Highland said the Vaccine Transformation Programme was a national three-year programme and it was at the early stages of implementing the government policy in its area.
The health board added that it would be making sure it did not do anything that increased risks to the population.
READ MORE: ‘Doctors of the future’ course starts to tackle rural GP crisisDr Philip Wilson, a GP and professor of rural health care, is opposed to the change.
He said the new clinics would be shared by different practices and there was a potential risk of some patients missing a clinic visit.
"There is a particular issue about remote communities getting occasional visits," he said.
"There are no powers for GPs picking up people opportunistically and increasing immunisation rates.
"There will be an immunisation clinic shared between several different practices, and the consequence of that is that even when patients want to have their immunisation and are able to turn up for the appointments they might have to travel huge distances to get there.
"That, in turn, is going to remove the incentive or make it more difficult for people to actually get immunisations."
Dr Wilson added: "It makes sense to carry on paying GPs to provide immunisations in rural areas."
Adam Strachura, of Age Scotland, said if the aim of the new set up was get more people inoculated then "that was a good thing".
But he added that for many older people their GP was key to their overall health and wellbeing.
He said: "Their regular GP is an important part of their health care needs. A GP will be able to look at all their medical issues, as well as administrating injections like the flu vaccination."
Laura Hamlet and her family live in Achiltibuie in Wester Ross. The community, 80 miles (129km) north west of Inverness, is 24 miles (38km) from the nearest village, Ullapool.
She said: "My youngest son is a winter baby, he was born in November, and winter babies tend to pick up lots of coughs and colds, so we had three goes at getting his immunisations."
The mother-of-two said that having to travel longer distances to reach a clinic would be more expensive.
She said: "You could end up having to put it off and in the meantime your child isn't immunised."
NHS Highland said it was not yet clear what changes, if any, would be proposed in rural areas of the Highlands.
A spokesman said: "Some areas in Scotland are further ahead with the changes such as Tayside and Lanarkshire and we are learning the lessons from that work.
"Any changes made in NHS Highland will be piloted first on a small scale before being rolled out.
"Childhood vaccine uptake in Highland, including for Measles Mumps and Rubella (MMR) is over 95%, and the population is well protected. Measles is a very rare infection in Scotland."
He added: "We work and will continue to work with Highland GPs and the Highland Local Medical Committee to explore how best to deliver vaccinations."