The Deputy First Minister also insisted there was no "bottleneck" in getting vaccines into the arms of Scots after it emerged that 334,871 people have been inoculated so far north of the border.
Opponents have claimed that more than 600,000 doses have already been allocated to Scotland, prompting a war of words between Westminster and Holyrood about availability.
The number of vaccine doses delivered remained broadly the same as yesterday, falling slightly from 25,327 to 24,962, the latest official figures show. The number of hospital cases saw the smallest rise since Christmas with 2004 patients, up 1, while intensive care cases rose five to 161. Positive tests also fell to 1634, although there were a further 89 deaths recorded.
GPs in Scotland have complained of "patchy" supplies of the vaccine and Dr Andrew Buist, chair of the BMA's Scottish GPs committee, said that allowing doctors to order stocks themselves would help "streamline" the process.
But Mr Swinney said: "The decisions we taken have been to put some structure into the way in which we order the vaccine and draw them down to create essentially fairness right across the whole country so that we can make progress in all areas of the country largely in a reasonably consistent manner.
"It won't be identical, but to give a bit of consistency and fairness across the country."
This is done through health boards in Scotland, unlike the clinical commissioning groups south of the border which cover bigger population areas.
But Mr Swinney said it was a "pretty similar outlook" across the UK, working from the wider supply chain down to GPs. He said the need to ensure "fairness" across Scotland my result in some "limitations over time" about how much supply can be put in particular areas because the vaccine comes in batches of 80 or 100.
"I understand completely that GPs want to be getting on with this," the Deputy First Minister added.
"But we're trying to get the vaccine to them as quickly, as evenly, as fairly, as consistently as we possibly can."
Currently in Scotland health boards provide order information for GP practices in their areas to National Procurement, who in turn pass this onto the distribution firm responsible for delivery. Once stock is released and an order has been placed, GP Practices will receive an automated email providing an indication of the delivery day.
The BMA has called on the Scottish Government to consider allowing GPs to order "directly" the supplies they need to vaccinate their patients.
Dr Buist said: “It is right for GPs to be involved in Covid vaccination in a way that best reflects their local circumstances, and also allows them to balance that with continuing to deliver vital care to their communities.
"At a national level – and at a regional level – this is the right thing to get the most effective vaccination programme in place. "However, that of course is dependent on GPs getting the supplies they need, when they need them, in order to make and deliver appointments.”
The medic said he is "optimistic" things will improve, but added: "It is important also to look at other ways to boost and give greater certainty to practices on supply – and providing GPs with the ability order directly is something that GPs have suggested could help the system work more smoothly. We have raised that with the Scottish Government – to see if it could work within the context of the overall agreement reached on delivering the vaccine – and await their response.”
It comes as a vaccine supply update obtained by the Scottish Conservatives sent to medics in Greater Glasgow and Clyde indicates that vaccine doses for the next cohorts - over 70s and vulnerable people who are shielding - may not reach GPs until February.
This would give GPs between a week and two weeks to meet the SNP’s mid-February target of vaccinating this group.
Tory health spokesman Donald Cameron said: “GPs and the BMA Scotland have warned all week that they are not getting vaccine supplies quickly enough.
“This letter raises even more troubling concerns that the SNP’s vaccine rollout is going too slowly.
“We need to know if this is only the case in Glasgow or across the whole country.
“GPs are coming forward with solutions and it’s vital the SNP look at every available option if they’re going to get back on track.
“The SNP have hundreds of thousands of doses of the vaccine sitting there ready to use but as it stands, they‘re struggling to reach their own targets.”
Labour interim leader Jackie Baillie said there are “real weaknesses” over the roll-out of Scotland's vaccination programme.
"When GPs say there is a problem with supply, SNP ministers should not stick their fingers in their ears - they need to listen and improve the system,” she added.
"The First Minister herself has said we are in a race against the virus, but she is in danger of getting stuck in the slow lane while the virus takes the lead."
Liberal Democrat health spokesman Alex Cole-Hamilton said: "GPs reckon they can get the rollout moving faster but the SNP are once again hoarding power in the centre.
"This shouldn't be about rivalry. It is in everyone's interest to get jabs in arms. I hope the Health Secretary will listen to what GPs have to say and consider putting their expertise to use."
A Scottish Government spokesperson added: “We are actively working to resolve any issues raised with us and will be happy to discuss with the BMA. We are grateful for suggestions from GPs and we will consider the proposal.
“This is a national vaccination plan, delivered locally, and health boards are an important part of ensuring vaccine supply reaches vaccinators.”