They have told researchers they felt they had "let their children down" by deciding to give their children the triple vaccine to ward against measles, mumps and rubella, despite assurances from scientists and doctors that it is safe.
Researchers from the Medical Research Council (MRC) said the parents also reported being let down by doctors, health professionals and health visitors over what they felt was unclear and inconsistent guidance over MMR.
The MRC yesterday called for better support for parents and understanding of the dilemmas they face when confronted with conflicting medical advice.
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It follows the controversy over the safety of MMR, linked in 1998 to autism by Dr Andrew Wakefield in a paper he published in the Lancet medical journal, leading to levels of MMR immunisation dropping.
Although those claims have now been largely discredited, the MRC study found that anxiety among parents with autistic children over MMR's safety have been slow to abate.
In what is thought to be the first time that parents' experience of the controversy has been researched, the MRC followed 38 parents of children with autism in 10 focus groups across the UK.
Shona Hilton, an associate researcher at MRC and one of the report's authors, said health professionals, parents and policy makers needed to be aware of the uncertainties parents face when making decisions about vaccinations.
"It's not only parents with autistic children but anyone with children that can feel anxious about what is in the child's best interest," she said.
Ms Hilton said, in addition to giving professional medical advice, doctors and other health professionals had to be attuned to the emotional strain that parents were placed under by the MMR controversy.
After Dr Wakefield's article was published in 1998, immunisation levels of MMR dropped from 92% across the UK to 80% in 2003-04, according to the Health Protection Agency. However, statistics published earlier this week show that immunisation rates in Scotland have begun to recover.
A spokesman for the Scottish Executive Health Department said: "It is a positive sign that the uptake of the MMR vaccination remains at a higher level than in recent times, as figures published earlier this week show. This is testament to the efforts of health professionals and parents in ensuring children are protected against the risks these diseases pose."
One of the parents involved in the MMR study said she felt uncertain about what the right choice over immunising her children was.
Laura Livingston, a bank worker, has two children, the youngest of which, Steven, has autism and learning difficulties. He was diagnosed six years ago, aged three, when controversy over the MMR jabs was at its height.
As a result, Mrs Livingston, from Knightswood in Glasgow, decided against giving Steven his MMR booster jab. But she says she does not know what she would do if she had to face the choice again.
"You're damned if you do and damned if you don't," she said.
Although she says her GP gave her impartial and helpful advice about whether to give her son his second MMR jab, she feels a lot of parents didn't receive this and were pressured into immunising their children.
Jab controversy
The controversy over MMR - the triple immunisation jab given against measles, mumps and rubella - flared up after a 1998 article by Dr Andrew Wakefield, published in the Lancet medical journal, alleging links to autism.
At a press conference to publicise the study, Dr Wakefield, a gastroenterologist, called for MMR to be replaced.
Subsequent studies have since failed to confirm the link and Dr Wakefield has faced widespread condemnation over his claims.
It has emerged that some children who took part in the research were also the subject of another study funded by legal aid to find out whether they had a compensation claim against the vaccine makers.
Dr Wakefield failed to disclose to the Lancet that he had received ยฃ55,000 from legal aid for the second study but denied a conflict of interest. He is due to face a disciplinary hearing before the General Medical Council in July.
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