The doses were wasted at Ayrshire Central Hospital in Irvine, North Ayrshire, on Saturday, while NHS staff were being vaccinated.
A source claimed that on at least two occasions, vials containing up to five or six doses had been disposed of after only one injection.
But in a statement NHS Ayrshire and Arran said the wastage was limited to three doses.
A source told The Herald: "We have always had suspicions that vaccines were being wasted.
"Given the crucial nature of the vaccination programme I found it ludicrous that such a thing would occur."
BMA Scotland warned of the 'risk' of vaccines going to waste due to appointment scheduling difficulties after vaccine dose spacing was extended at short notice from three to 12 weeks.
It has also called for "full transparency" about vaccine wastage.
A spokesman for NHS Ayrshire and Arran said: "Vaccines are being administered by experienced immunisation staff who have received additional training for the safe preparation and delivery of the COVID-19 vaccines.
"At this stage in the rollout Ayrshire and Arran has seen negligible numbers of wastage thanks to the skill and dedication of our immunisation team.
"Vaccinations took place at Ayrshire Central Hospital last weekend (23-24 January).
"Three vaccine doses were recorded as wastage from this vaccination session.
"We have reviewed our existing processes to ensure the continued minimisation of waste.
The Scottish Government has said that early estimates suggest vaccine wastage in Scotland has been around 1.82 per cent, which is "well below a 5 per cent planning assumption".