Parents fear a link between MMR and autism
Dr Mac Armstrong's plea to parents to immunise their children comes as new figures show that one in eight toddlers have not received the triple MMR injection.
Growing numbers of parents are choosing not to have their children vaccinated with the combined vaccine because of fears it causes bowel disorders and autism.
Figures from NHS Scotland showed that at the end of September this year, 13% of two year-olds had not been immunised with the vaccine.
But the Scottish Executive continues to insist that the combined jab is the safest.
Dr Armstrong said the time lags between three separate injections left children at risk of death or serious illness.
Ninety-five per cent of children need to be vaccinated to avoid the spread of the three illnesses.
Dr Armstrong said expert advice from around the world showed MMR was the safest and most effective way to protect children.
"We want to re-assure parents about the safety of the MMR vaccine and continue to recommend it as the most effective way of protecting children from these three potentially serious diseases," he said.
The Scottish Parliament's Health and Community Care Committee published a report on March 28 this year saying there was "no proven scientific link between the MMR vaccine and autism".
Dr Armstrong said: "Offering single vaccines, with the suggested time lags between the three, would leave a child at risk from mumps, measles or rubella, which could result in death or serious illness."
He said children would also suffer increased trauma with three jabs between 12 to 18 months and another three injections, instead of one booster, between the ages of three and five.
He added: "It is therefore vital that we now start to reverse the current downward trends in uptake rates and return to a level of around 95%, which is required to ensure we protect all children and avoid the spread of these illnesses."