Children in the UK will get a Covid vaccine only if they are over 12 and extremely vulnerable, or live with someone at risk, as scientists raised concerns about inflammation around the heart linked to the Pfizer jab.

Sajid Javid, the health secretary, said he accepted the advice of scientific advisers that only children over 12 with severe neuro-disabilities, Down’s syndrome, immunosuppression and multiple or severe learning disabilities should be allowed to get the Pfizer vaccine. Children over 12 who live in the same house as people who are immunosuppressed will also be eligible for jabs.

The opinion of the Joint Committee on Vaccination and Immunisation (JCVI) expands the eligibility for children, after a previous decision that vulnerable 16- and 17-year-olds could get vaccinated.

Some ministers had signalled that all over-12s could start a programme of being vaccinated from September, contributing to population-wide immunity against Covid.

However, the advisory body said: “The health benefits in this population are small, and the benefits to the wider population are highly uncertain. At this time, JCVI is of the view that the health benefits of universal vaccination in children and young people below the age of 18 years do not outweigh the potential risks.”

The Pfizer vaccine has been authorised for people aged 12 years and over in the UK by the Medicines and Healthcare products Regulatory Agency.

However, the JCVI highlighted “emerging reports from the UK and other countries of rare but serious adverse events, including myocarditis (inflammation of the heart muscle) and pericarditis (inflammation of the membrane around the heart), following the use of Pfizer/BioNTech BNT162b2 and Moderna mRNA1273 vaccines in younger adults”. The scientists also said the risk of long Covid was “very low in children”.

Javid said he had asked the NHS to prepare to vaccinate those eligible as soon as possible and wanted the JCVI to keep vaccination for children under review.

The decision has split scientists, many of whom had expected the Pfizer vaccine to be given the green light for over-12s.

Dr Stephen Griffin, a virologist from the University of Leeds, said: “It’s unclear what the JCVI knows that the MHRA doesn’t,” noting that many countries had begun vaccinating children aged 12 and above.

“There does seem to be a link with vaccines and myocarditis but it’s very mild and very rare – but with Covid, there is a risk of long Covid,” he said.

Gabriel Scally, a visiting professor of public health at the University of Bristol and a member of Independent Sage, said the JCVI decision was “not logical”, noting that the vaccine had been authorised as safe and effective for over-12s by the MHRA and was being used in this age-group in a number of countries.

“Yes, there are some side-effects, but they are treatable,” he noted, highlighting that there was no evidence that the vaccine had caused any deaths in this age group, while Covid has in rare instances.

But Prof Adam Finn, a professor of paediatrics at the University of Bristol and a JCVI member, said there was pretty much “incontrovertible evidence” emerging that the heart inflammation was a real safety signal, although the number of serious cases was “very, very small”.

Overall, instances of this heart inflammation are about one in 100,000, said Jeremy Brown, a professor of respiratory infection at UCL and a JCVI member, cautioning that there was not a lot of data at the moment. However, he said, the incidence of these types of side-effects was more prevalent in boys than girls, and at the older end of the adolescent spectrum than younger.

School leaders warned of more disruption to education next autumn. Geoff Barton, the general secretary of the Association of School and College Leaders, acknowledge the need for caution but said it “leaves us with the potential for very high numbers of infections among children in the autumn term particularly given the relaxation of wider restrictions in society”.

“This could mean yet more educational disruption as well as causing wider public health concerns. It is therefore imperative that the government places an intense focus on supporting schools and colleges with Covid protection measures.”