Now, with calls mounting for an alternative to be offered on the NHS and suggestions that the controversy may be leading to an increase in measles cases, the Government appears to have 'taken the PR gloves off' as one observer put it, and fully joined the battle.
The most obvious sign that the Government was stepping up its comms campaign was a press conference last week in which Department of Health chief medical officer Professor Sir Liam Donaldson and other experts issued a robust restatement of the health department that there was no evidence of a vaccine-autism link.
Tony Blair has thrown his personal weight behind that position, saying he would not ask parents to give their children something he would not give his own - interpreted as a clear hint to those demanding to know if baby Leo had had the vaccine.
But in the face of all the press coverage and statements being made, the DoH is seeking to play down the importance of its latest PR moves.
Since last year DoH and Health Promotion England - the part of the NHS concerned with proactive healthcare messaging - has been in constant communication with GPs, health visitors and health practice nurses on this subject throughout the health trade press.
This initiative is now to be extended with a press campaign reiterating Donaldson's position and TV ads in support of the concept of vaccinations generally.
A DoH spokesman said: 'We are forging ahead with a campaign we have been running. We are trying not to participate in scaremongering and hysteria but to remain calm. We want to spread appropriate information as widely as possible.'
The MMR vaccine is made by FTSE 100 pharma giant GlaxoSmithKline. Its spokespeople have been firmly pushing the safety line, in the face of growing calls for parental choice backed by the Royal Free Hospital's Dr Andrew Wakefield, whose research was the first to question the triple jab's safety.
The various protagonists have reached the same conclusion about what a peculiarly difficult communications problem MMR represents. If nothing is said in defence of the vaccine, the long-term take-up of MMR will continue to fall, leaving children unprotected and allowing measles to spread.
Anything that is done, however, is perceived among the general public as medical 'experts' bullying ordinary parents who have concerns about their children, and is counter-productive.
British Medical Association head of comms Nigel Duncan says: 'This is positioned as vulnerable parents versus the establishment. The Government is in a tricky situation. The more it puts the great and the good up as experts, the more it makes it the might of establishment versus a lone voice.'
That lone voice is not, in fact, alone at all, but is the sound of a concerted PR push by campaigning body JABS - Justice Awareness and Basic Support. It was formed in 1993 by a group of parents who believed their children had been affected by the MMR vaccination and has been campaigning steadily ever since.
Ann Coote, a founder member who describes herself as a 'housewife', says: 'Parents feel as if they are being bullied into doing something they may not want to do. It is David taking on Goliath - a lot of people have come down on the side of the underdog.'
Based in Warrington, JABS seems to get much of its effectiveness from the fact that it is outside the normal media and political circles of London and is motivated by a mix of personal involvement and genuine concern.
One senior national newspaper health correspondent says of the sudden rush of coverage in the papers: 'This is about parents going out of their head because their kids have been diagnosed with autism. They are looking for an answer. If you feel you can do something to warn others when something like this happens to you, you feel better about life.'
Such an emotive approach is clearly difficult for government communicators to address.
The journalist has some sympathy for the Government's plight: 'It has done all it can in PR terms, but there is such an emotional wash on the other side that the Government is not being listened to properly. It is hard to counter the arguments.'
JABS began to attract media support from the mid-market tabloids last year following publication of Dr Wakefield's work on a link between MMR and autism.
Nurtured by JABS, together with groups such as the National Autistic Society (NAS) that have also been calling for single jabs to be made available, the media outcry has grown. The Leo Blair story and publication of fresh research has helped to keep the matter in the public eye.
The NAS says it was the increase in measles cases, after months of warnings from the DoH about falling vaccination rates, that finally put the matter on the front page. The hope within Whitehall must be that the story will now finally go away.