Some areas had less than 80% take-up of the injection
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The number of children receiving the three-in-one MMR jab still falls below recommended levels, it has been warned.
Experts advise that 95% of children should be immunised for the general public to be protected against measles, mumps and rubella.
Quarterly figures show uptake is still well below this "herd immunity" level, at 90.9% of two-year-olds.
However, the Scottish Executive said it was encouraging that uptake was higher than in recent years.
The figures are still lower than the 97% of two-year-olds who have been immunised against polio, diphtheria and tetanus.
There were also large regional variations, with particularly low take-up rates in the Highlands and Islands.
In the Shetland health board area the rate was 76.6%, while in Highland it was 77.9%, 85% in the Western Isles and Orkney 84.8%.
The rate for Greater Glasgow was 91.2% while the highest figure, 93.5%, was found in Dumfries and Galloway.
The uptake rate for MMR slumped in the wake of a controversy which linked the jab to autism and the bowel disorder Crohn's disease.
Choice call
It was announced on Monday that the doctor who first suggested a link between the MMR vaccine and autism is to be charged with serious professional misconduct.
Dr Andrew Wakefield's research was published in the Lancet in 1998 but has now been widely discredited.
A Scottish Executive spokesperson said: "These figures show that the uptake of all childhood vaccinations remains strong.
"The uptake of the MMR vaccination remains at a higher level than in recent times.
"This is a positive sign and testament to the efforts of health professionals and parents in ensuring children are protected against the risks these diseases pose."
Scottish Conservative health spokeswoman Nanette Milne said the shortfall in protection was concerning.
Ms Milne said her party believed MMR was the most effective way to tackle measles, mumps and rubella but called for more support for people choosing single vaccinations.
She said: "This choice must be extended to the parents of every child by making the single vaccine free on the NHS.
"It is simply not right that only the better off can afford to choose and I hope the health minister will back our repeated calls to stop ignoring the plight of the poorest in society, who cannot afford to choose."