The number of two-year-olds who received the jab in the quarter ending 30 June rose by one per cent to 88.6% over the previous three months.
The figures were released by the NHS as one expert fuelled the debate about links between the combined inoculation and autism.
Christopher Gillberg, professor of child and adolescent psychiatry at St George's Medical School, London, said the controversy had hampered research into autism.
The focus on the effect of the triple vaccine had stymied potentially far more fruitful avenues of research into a condition which is still little understood, he said.
Scotland's chief medical officer Dr Mac Armstrong welcomed the new figures, which took the MMR immunisation rate to its highest level since March 2001.
Immunisation rates for other childhood vaccines continued to be above the desired 95% mark, he said.
Immunisation rates
"In terms of MMR, we understand parents' need to be well informed about issues concerning the health of their children, which is why the Scottish Executive issued its new MMR Discussion Park late last year," Dr Armstrong went on.
"We are sure that this is proving to be a useful tool in helping healthcare professionals discuss issues of concerns with parents and convince them that MMR is the most effective way to protect their children from these three childhood diseases."
Dr John Garner, the chairman of the British Medical Association in Scotland, said he hoped immunisation rates would continue to rise.
He said that he understood parents' concerns about the safety of the vaccine.
But he stressed: "The BMA believes that the combined MMR vaccine is the most effective way to protect children against the potentially fatal disease of measles, together with mumps and rubella.
"We remain anxious that there are still not enough children receiving it."
Dr Pat Tookey, an expert in rubella who is in Glasgow to speak at a conference on the effectiveness of MMR, said: "The problem with introducing choice in terms of taking up single vaccines is that children would remain unprotected against these diseases for longer.
"The longer you leave children susceptible to something like rubella then the more likely it is that rubella will start to circulate again."