Figures from Public Health Scotland (PHS) show 983,875 adults have not received a third dose or booster, six months after the programme began. More than 500,000 of these are at least 12 weeks on from their second dose.
The Scottish Government admitted fewer appointments had taken place than expected, after PHS reported that 21,000 vaccine doses were thrown away in February after reaching their expiry dates.
A senior health official has urged members of the public to come forward for third doses, as a study led by Glasgow Caledonian University found protection from two doses reduced “considerably” after six months.
It comes as record numbers of people are in hospital with Covid in Scotland.
“It beggars belief that when we've got such high case numbers and we've got such high occupancy in hospital with people still becoming seriously unwell, that people aren't coming forward for that third dose,” she said.
“We're open and available, and you don't have to take a lot time off work to come and get it.
“It's still protecting you against severe illness so it makes sense to get it, and the impetus should be there now given how difficult things are right now.”
She added: “While we're paying so much attention to vaccination and maybe looking ahead to the fourth dose, there are still so many people who haven't even had their first booster and to do so would protect them.
“It would just be great if they could come forward.”
A study of 35,768 health workers – 6,000 from Scotland – published in the New England Journal of Medicine found that protection from two doses of vaccine began to wane “considerably” after six months.
Glasgow Caledonian University Professor Lesley Price, who led the Scottish arm of the study, said it “reinforces the need for booster jabs”.
“We need to keep monitoring people’s immune response to the booster so that the government can make appropriate decisions about their future vaccination strategy,” she said.
"The importance of this has been recognised with the study now continuing to follow up its participants for up to two years.”
A Scottish Government spokesperson said: “Scotland currently has the highest overall percentage vaccination rates for first, second, third doses and boosters for those aged 12 and over, of any UK nation and we thank everyone who has come forward to be vaccinated. All those who are eligible have been offered an appointment and 86.6 per cent of eligible adults have now received a booster.
“The vaccination programme is still ongoing as we continue to provide jags to strengthen protection from Covid-19 to keep individuals and families safe. It's never too late to receive your booster – or even a first or second dose – and we would encourage anyone yet to be fully vaccinated to come forward.
“There is capacity right across Scotland to get vaccinated and online booking and links to local drop-in arrangements can be found on NHS Inform or via the national helpline.”