Experts say it is perfectly safe, but vaccination rates dipped following controversy about its safety.
A study which raised the possibility that MMR was linked to autism has since been dismissed by the vast majority of research, but levels of public confidence in the jab have still not fully recovered.
In a letter to all PCTs, the Chief Medical Officer Sir Liam Donaldson asks health bosses to urge parents to get their children immunised.
An average PCT will receive £30,000 to help fund the catch-up campaign.
In London, PCTs will receive £60,000, reflecting the higher numbers of children who have yet to be vaccinated.
Rising cases
The number of cases of measles in England is rising following a decade of relatively low vaccine uptake.
We cannot stress too strongly that all children and young people should have the MMR vaccine
Dr Patricia Hamilton Royal College of Paediatrics and Child Health
In 2006 and 2007 there were 1,726 confirmed cases in England and Wales - more than the previous 10 years put together.
From 1996 to 2005 there was a total of 1,621 confirmed cases.
It is estimated that around three million children aged 18 months to 18 years have missed either their first or second MMR vaccination.
Scientific advice from both the Department of Health and the Health Protection Agency suggests vaccination levels need to be increased as a matter of urgency.
The previous success of the MMR vaccination programme reduced the number of measles cases to very low levels for a number of years.
Between 1992 and 2006 there were no deaths from acute measles in England. However there was one death in 2006 and another in 2008.
Professor David Salisbury, director of immunisation at the Department of Health, warned that it was vital that MMR vaccination rates were increased.
Target rate
Around 95% of the population need to be vaccinated to protect against widespread outbreaks of measles.
The current vaccination rate across England and Wales is around 10 percentage points lower.
In Scotland and Northern Ireland, uptake of the first dose of MMR is higher, at approximately 91%.
2002 - Health experts blamed rise of measles cases on poor uptake of MMR vaccine
2005 - Mumps epidemic mainly affected 13-24 year-olds who were too old to have had MMR vaccine as children<
Professor Salisbury said measles was among the most easily spread of viruses.
He said: "Measles is serious and in some cases it can be fatal. Delaying immunisation puts children at risk.
"If we continue to accumulate unvaccinated children measles will spread among them - at some point there will be a measles epidemic."
He stressed: "The evidence on MMR is absolutely clear - there is no link between the vaccine and autism."
Dr Patricia Hamilton, president of the Royal College of Paediatrics and Child Health, said: "We cannot stress too strongly that all children and young people should have the MMR vaccine.
"Overwhelming scientific evidence shows that it is safe."
The Department of Health says around 10% of measles cases require hospital admission and one in 5,000 are fatal.
Wales has no plans for a similar catch-up campaign.
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