Covid boosters will be offered to all over-50s and those at severe risk of the disease as part of the “toolbox” of measures for controlling coronavirus over the autumn and winter following guidance from the government’s vaccine advisers.

The Joint Committee on Vaccination and Immunisation (JCVI) said a third dose of vaccine would top up the immunity in those whose protection had likely waned since they completed their first round of shots earlier in the year.

Data from the UK suggests that protection provided by two shots of the Pfizer/BioNTech or Oxford/AstraZeneca vaccines wanes within six months, though it is unclear what impact this has on cases of severe disease.

Researchers on the Zoe Covid study at King’s College London recorded falls in protection after two shots of Pfizer vaccine from 88% at one month to 74% at five to six months, and from 77% at one month to 67% at four to five months for the AstraZeneca vaccine.

The JCVI recommended that all over-50s and at-risk groups receive a booster of the Pfizer jab regardless of the vaccine they received first time around, to be given at least six months after their second dose. While the advisers stated a preference for the Pfizer shot, an alternative is a half dose of the Moderna vaccine – the amount Moderna is proposing for boosters in its applications to European and US regulators.

The rollout of Covid vaccines started with the nine priority groups including elderly people, the clinically extremely vulnerable and health and social care workers in December last year, and immunity in these people is expected to have waned the most.

Under the JCVI guidance, boosters will be offered to the same nine priority groups, working down the groups in order as before. The under-50s may not need booster shots as younger people tend to produce stronger immune responses, but the JCVI is to conduct more work on the question.

Interim advice from the JCVI in June urged the NHS to prepare for a booster programme starting as soon as this month, but ministers were keen to receive the advisers’ final recommendation before going ahead. The Medicines and Healthcare products Regulatory Agency (MHRA) has approved the Pfizer, Moderna and AstraZeneca vaccines for use as boosters.

The JCVI in turn was awaiting data from a number of major studies including the UK’s Cov-Boost study, which assessed the extra protection afforded by third doses of several different vaccines.

Speaking on BBC Radio 4’s Today programme, the vaccines minister, Nadhim Zahawi, said the government had accepted the final advice of the JCVI and that Covid boosters would be given at the same time as flu shots where possible.

“This is probably the last piece of jigsaw to allow us to transition this virus from pandemic to endemic and I hope by next year we’ll be in a position to deal with this virus with an annual inoculation programme as we do with flu,” he said.

The move follows an announcement on Monday from the UK’s chief medical officers recommending Covid vaccines for all 12- to 15-year-olds, a decision reached after reviewing the broader impact of such vaccinations on children’s health and education. While the risk from Covid is very low in the age group, some children do get ill, and widespread vaccinations are expected to reduce transmission and the number of school outbreaks that disrupt education.

The rollout of boosters has proved a controversial issue given that many other countries have not yet had sufficient supplies to vaccinate their most vulnerable. An expert review published in the Lancet on Monday by an international group of scientists, including some at the WHO and FDA, found that, even for the Delta variant, vaccine efficacy against severe Covid is so high that booster doses for the general population are not appropriate at this stage.