The proportion of children vaccinated against measles, mumps and rubella at 24 months has fallen in England for the first time in seven years.

By their second birthday, 92.3% of children received a first dose of the MMR vaccine, down from 92.7% the year before, data from the Health and Social Care Information Centre (HSCIC) for 2014-15 shows.

The percentage of children vaccinated remains short of the World Health Organisation target of 95% needed for herd immunity – the level at which a measure of protection is provided for individuals who are not immune.

MMR coverage was highest in the north-east of England (95.2%) and lowest in London (87.3%).

In a slight increase on the previous year, 88.6% of children had received their second and final dose of MMR by their fifth birthday, while by the same age 94.4% of children had received their first dose.

Uptake of the MMR vaccine fell heavily in the late 1990s following the publication of research by Andrew Wakefield suggesting a possible link between the vaccine and autism. Experts have widely discredited his study and he was struck off the medical register in 2010.

The HSCIC report said several factors could have led to a rise in MMR uptake in recent years, including campaigns to target unvaccinated teenagers and a recommendation that MMR is offered on the same day as other vaccines. But experts suggested the new drop could be due to problems with the study’s methodology, potentially linked to increased pressure on NHS staff.

Overall, the figures for most routine childhood vaccinations at the ages of one and two fell slightly in 2014-15 for a second consecutive year, but there were small increases in the numbers vaccinated by the age of five.

The flu vaccine was also offered to all children aged two, three and four during the winter of 2014-15. Coverage for all two-year-olds in England was 38.5%. It was 41.3% among three-year-olds and 32.9% among four-year-olds. Among adults aged 65 and over, flu vaccine uptake was 72.7% in 2014-15, down on 73.2% the year before, and below the WHO target of 75%.

David Elliman, an immunisation expert for the Royal College of Paediatrics and Child Health, said: “It is disappointing that uptake of NHS immunisations has not continued to rise, however the falls are very small. This could be read as children not receiving the vaccination or, alternatively, it could be a lack of data collection linked to considerable pressures on staff working in the NHS.

“Immunisation is vitally important if we are to protect child health both here in the UK and internationally in the long term. I would therefore urge all parents to contact their GP if they are unsure whether their child is up to date with their vaccinations.”

Mary Ramsay, the head of immunisation at Public Health England, said: “England has a world-class national immunisation programme which is constantly reviewed and updated to reflect the changing nature of infectious diseases, and the annual data shows continued high uptake of all routine vaccinations in children aged up to five years.”

She added: “We urge all parents to check that their children are up to date with their vaccinations and to contact their GP as soon as possible if they are unsure so that no child misses out.”