Only 86% of two-year-olds have received the triple jab
Doctor Eileen Ruberry, who headed the 1994 Department of Health committee, told BBC Radio 4's Today programme that the triple-jab policy was "not working".
Take-up of MMR has declined since suggestions were made of a link between it and autism or bowel disorders.
According to the latest figures, 86% of two-year-olds have received the triple MMR injection as opposed to 97% of children who have received the tetanus inoculation.
Dr Ruberry said more children would be vaccinated against MMR if parents could choose single jabs.
"Parents would not feel pressurised. They could think about the situation and make an informed choice rather than making an emotional judgment," she said.
'High price'
"If they are given the choice...but that nevertheless the recommendation is that the triple vaccine is the best option, then I actually suspect most parents will go for the triple vaccine."
Conservative MP for Bromsgrove Julie Kirkbride, who has campaigned for wider access to single jabs, said: "I am delighted this senior doctor has shown such commonsense."
But the Liberal Democrat health spokesman, Dr Evan Harris, said a reversal of policy would "undermine the confidence of the vast majority of people who are still having the MMR".
"MMR is safe and very effective and single vaccines are less effective and there is less evidence of their safety," he said.
"When there was a whooping cough scare - based around stronger evidence than the scare around MMR - the government did split the vaccine and the coverage level significantly dropped, children got infected and children died.
"That is too high a price to pay in the name of more choice."
But Dr Ruberry said people's approach to public health issues and doctors has changed
"People want to have the choice," she said.
"They do not like to be dictated to. They expect to be treated in a non-paternalistic way.
"That is quite different from 20 years ago when we were considering the whooping cough vaccine."