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Two primary schools on Sheppey and one in Sittingbourne are to ignore the government's request to allow Year One and Year Six pupils to return to their classrooms on June 1.
The Island Learning Trust, which runs Minster and Halfway Houses primary schools on Sheppey and Sunny Bank Primary School in Sittingbourne, has sent a letter to parents explaining its decision.
Chief executive Debbie Wheeler said: "After considering the guidance and the parent survey outcomes (only 14% wanted to send their children back) we will not be re-opening for years 1 or 6."
The trust says its main concern for the youngest children is not so much social distancing but security and safety.
She said: "The alteration to the classrooms would not allow us to offer an acceptable experience; tables being used for one pupil, no displays, no soft furnishings, no toys, no shared resources, not being able to mix with friends.
"Add to that separation anxiety, attachment issues that this period at home could have created, and the distancing means we cannot adequately provide comfort."
She asked: "How are parents going to hand over these young children at the school gate?
"The trust board also believes social distancing for the youngest pupils is not possible. We feel this would actually be harmful to pupils at this age at the moment."
The trust says bringing back Year 6 would be "detrimental to their school experience" as they already said their 'goodbyes' in March.
Mrs Wheeler added: "They should be having a prom, creating an assembly or play for parents and going on a trip. None of these things are now possible.
"They would be in a bubble of eight with one staff member all day unlikely to be their current class teacher.
"For us this is not only sad but quite demoralising. They would be coming back to experience dejection at the end of their primary school life."
The schools will, however, prepare to take back Year 5 pupils from June 15. All pupil groupings will be based on eight to allow 2m social distancing.
Staff will be wearing a face mask, apron and gloves.
Provisions for key-worker and vulnerable children will continue.
Listen to our podcast on the debate around schools reopening