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An entire year group will not return to class until next year after a child tested positive for Omicron.
Parents were informed on Thursday morning that a pupil from Hampton Primary in Herne Bay was found to have contracted the variant.
Despite this, bosses were advised by Public Health England and the Department for Education that youngsters in the same age group, Year 3, did not need to be collected from the Fitzgerald Avenue site early.
Instead, head teacher Yvonne Nunn was told not to close the year-group bubble and to urge the parents of eight- and nine-year-olds to book a PCR test within the next 24 hours.
But following talks with other "lead professionals" the same day, she ordered every Year 3 child to self-isolate immediately.
"Please be assured I sought guidance from all relevant bodies and was told not to close the bubble and to advise booking of PCR tests," Ms Nunn wrote in a letter to parents.
"However, these recommendations do not follow the government guidance above and I have since spoken to the local authority, who have agreed that all close contacts should self-isolate for 10 days.
"The guidance clearly states that those identified as a close contact should book a PCR test and self isolate for 10 days up until December 18.
"We have identified that close contacts are all our Year 3 children and children attending Breakfast Club."
All Year 3 parents and carers were told to pick up their children and book PCR tests as soon as possible.
The same advice was issued to all other youngsters who attended the school's breakfast club over the last two weeks.
They will be forced to miss classes over the rest of term, which ends on December 17, and will not be able to return until lessons restart in the new year.
Ms Nunn also revealed that she has decided to cancel the school's Christmas service at Christ Church St Andrew's in William Street in the wake of the positive test.
"The rise in Covid cases has crept up on us again and now the confirmed case of Omicron in Year 3 has forced us to make this very difficult decision to remove the possible risk of infection being spread among audiences," she explained.
"I am deeply saddened for our children and families who have been denied this opportunity for another year.
"Children in school will perform the Christmas service in their bubbles at school, and these performances will be recorded and posted onto our website."
So far, 23 cases of the new Covid variant have been confirmed in Kent, with another 151 probable infections.
The Canterbury district - which includes coastal towns Herne Bay and Whitstable - has the joint-highest number of confirmed Omicron cases in the county, with five.
Government figures also show the specimen date for the first positive tests for the variant across Kent were in Dartford and Medway on November 22, two days before the strain was reported in South Africa.