Concerns have been raised that NHS staff, who are included in the first priority groups for the jab, will not accept the vaccine, putting both themselves and patients at risk. Only about a fifth of NHS workers have the seasonal flu jab, and surveys suggest almost half of nurses will not have the H1N1 vaccine.
But Dr Harry Burns yesterday sought to encourage staff to have the jab, alongside the at-risk groups.
When asked about the decision by some healthcare professionals to shun the vaccine, Dr Burns said: "It is hugely misguided. The benefits far outweigh the risks."
Concerns have been raised about possible side-effects linked to the swine flu jab.
The vaccine has been added to the UK's Vaccine Damage Payments Scheme, which gives pay-outs to people severely affected by vaccinations. However, experts have said any reactions linked to the vaccine are likely to be mild.
The Medicines and Healthcare products Regulatory Agency (MHRA) said the most common side-effects in some people would be pain, swelling or redness around the site of the injection. Other reactions could include headaches, dizziness, muscle aches, mild fever and fatigue.
The MHRA will be monitoring any suspected side-effects due to the swine flu vaccine as part of its Adverse Drug Reaction website.
Experts will investigate if problems experienced are linked to the vaccination or are merely coincidental.
Health secretary Nicola Sturgeon said: "We know from previous experience with the seasonal flu vaccine that not all frontline health workers take up the jab. Obviously, this is concerning, and we would encourage everyone who is offered the vaccine, including health workers, to get it.