On Wednesday night, officials admitted the new advice may slow the rollout’s progress amid concern it could undermine confidence.
But scientists said it was crucial that they were “honest with the public” about the uncertainties of the programme, including its “extremely small” risks and “modest benefits”.
Twelve to 15-year-olds are currently only offered one dose of a Covid vaccine.
The precaution was taken because of evidence from other countries linking most cases of myocarditis to second jabs. However, most nations have shorter intervals between doses.
On Wednesday night, JCVI members said the rollout of jabs to adults in Britain – with a gap of between eight and 12 weeks – suggests that, with a longer interval, there is almost no risk of myocarditis.
The scientists said it seemed possible that, among those who had been naturally infected, a three-month gap might similarly reduce such risks.
Prof Adam Finn, a member of the committee, said the advice had been changed in the light of emerging evidence.
“There are voices pushing for a much more black and white kind of line on this, that the public are going to be better off if we could give an absolutely clear and unequivocal message,” he said.
“In a way we’d love to be able to do that, but it’s not good if it’s not true. Ultimately, the whole value of the programme, and of all of our other programmes is that we’re honest with the public.
“There are uncertainties around it – the risks are extremely small, but they exist, and the benefits are modest.”
Prof Finn also said it was likely that the committee would recommend second doses for 12 to 15-year-olds in the future.
Earlier this week, it announced that 16 and 17-year-olds will start to be offered second doses after a 12-week gap.