It comes after a request for help from all mainland health boards made in mid October.
A total of 121 Armed Forces personnel will be deployed to the task this week, including 100 vaccinators, 15 nurses, and command and support staff.
They will join 86 personnel working in acute care with NHS Lanarkshire and NHS Borders, alongside others deployed to the Covid-19 testing programme, and the Scottish Ambulance Service.
The Scottish Government has also asked for support for two other health boards, NHS Grampian and NHS Ayrshire and Arran.
Armed Forces personnel were previously brought in to help in some health boards during the first round of vaccination.
Opposition politicians have repeatedly called on the Scottish Government to speed up the flu and Covid-19 booster programme, which has progressed more slowly than forecast.
All over-50s, unpaid carers, everyone over 16 with an underlying health condition and adults in the same household as anyone immunosuppressed were due to be invited for a third jag from October, but this has been changed to mid this month.
Health secretary Humza Yousaf said: “We are now in the midst of an extremely busy period for the national autumn/winter vaccination programme with flu and Covid-19 booster injections being offered to the most vulnerable groups, alongside first Covid-19 jabs to 12-15-year-olds.
“With increasing levels of social mixing and close social contact in the colder months, it is expected that Covid-19 will add to the winter pressures usually faced by the NHS. That is why we have again requested military support to complement our existing resources and to ensure we can get even more vaccinations into arms as quickly as possible.
“It remains clear that getting vaccinated is the single most effective step that anyone can take to protect themselves from the most severe disease caused by Covid-19.
"Anyone who has not yet received their first or second Covid-19 vaccination can check their nearest open access centre on NHS Inform or phone the national vaccination helpline on 0800 030 8013.”