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Sajid Javid said consent will be sought from parents of 12 to 15-year-olds over the coronavirus jabs.
But if an agreement cannot be reached on whether a competent young person should receive the vaccination, the child’s decision “will prevail”.
Mr Javid told Sky News: "If there is a difference of opinion between the child and the parent then we have specialists that work in this area, the schools vaccination service.
“They would usually literally sit down with the parent and the child, and try to reach some kind of consensus.
"If ultimately that doesn't work, as long as we believe that the child is competent enough to make this decision then the child will prevail."
Covid vaccines for healthy children aged between 12 and 15 are not being recommended by the Joint Committee on Vaccination and Immunisation (JCVI).
The JCVI found the jab should not be offered to the young age group on health grounds alone.
But it did advise the government look at "wider issues" including the impact of the virus on schooling.
The UK’s chief medical officers are currently reviewing the matter.
A final decision on whether the vaccines will be offered to the age bracket is expected to be "in the coming days", Mr Javid added.