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Head teachers have been told to make sure they understand coronavirus guidelines so pupils and staff are not sent home "needlessly".
The intervention by Kent County Council's education chief, who wrote to all heads, comes as an increasing number of schools have either closed entirely or told whole year groups to stay away, causing problems for parents.
It came on the day nine schools in the county announced they were closing after a rising number of coronavirus cases, including in Sittingbourne, the Isle of Sheppey, Canterbury, Dartford and Medway.
The authority's corporate director for children, young people and education Matt Dunkley explained he understood it was becoming difficult for schools in areas with high infection rates to continue to deliver high quality education.
He added how the council is sympathetic with the pressure head teachers are facing with the anxieties of parents and staff, while tackling something which can change on an hourly basis.
Mr Dunkley said: "While it remains the case that decision making on the running for your schools is for you to take with your governing bodies and Trusts, it is becoming clear that there are considerable differences in decision making at a locality level, and that does cause some problems at community level, and for some families.
"Quite simply, it is perceived that some schools are closing when other local schools facing similar or the same challenges are not."
The KCC chief added he knows "no one has taken the decision to close lightly" and that some schools are only notifying the council after making their decision.
Mr Dunkley said: "Can I ask you to ensure that you are clear on the requirements and what is meant by close contact so that individuals and bubbles are not sent home to isolate needlessly?
"In many cases a number of the parents in schools where a decision has been taken to move to remote learning are teachers and teaching assistants in other local schools, or work for the NHS or in another health or vital community role, and the knock-on effect in that community is considerable.
"I am sure you will have gone through the many stages of decision making prior to taking a decision to move to full remote learning for your pupils and students - engaging supply, re-timetabling lessons and restructuring staffing, zooming lessons into classes managed by TAs and many other alternatives that you would not have believed possible in better times.
"I would also expect that where you know you are close to having to consider a decision to move to full remote learning, that local conversations with neighbouring schools take place."
KCC was asked to comment further on the letter but declined.
Hundreds, if not thousands, of pupils are now at home as more schools and year groups close.
Responding to the letter, Alan Brookes, executive head of Fulston Manor School in Sittingbourne, one of those to have shut, said he did not believe any head took the decision to send pupils home without exploring every other possible avenue first.
"At Fulston Manor, we have rigorously applied all DfE guidelines, taken on additional staff, organised cover for absent colleagues and so on.
"Advice has been sought at every juncture from the Department for Education, the Local Authority, the Regional Schools Commissioner and Public Health England, who confirmed on Sunday that a full closure was a justifiable decision.
"The welfare and safety of all members of a school community are of paramount importance to all head teachers and a failure to act decisively in situations such as this is not an option."
"It should be emphasised that the position of every school will be different and that it is the head teacher who is best placed to decide what is right for their own school."
Mr Brookes, who is also chairman of the Kent Association of Headteachers, added: "None of the measures taken short of full closure managed to stem the alarming rise in the number of positive tests being reported by staff and students, which have continued to increase significantly over the past 48 hours.
"There are now nearly 30 confirmed cases amongst staff and students and over 40 teachers unable to attend work either because of positive tests or because they have been contacted and required to self isolate.
"The welfare and safety of all members of a school community are of paramount importance to all head teachers and a failure to act decisively in situations such as this is not an option."
Mr Brookes said while he regretted the further disruption to pupils' education, their health had to come first.
"The overwhelming number of messages of support from our parents that we have received since Sunday is a clear indication that they too recognise this priority and that the decision taken was the correct one under these exceptionally difficult circumstances," he added.
Simon Cox, executive head teacher at Westlands School in Sittingbourne, which has seen at least 19 positive Covid cases since September, said Mr Dunkley had made some valid points.
"The tone appears to encourage schools to stay open where possible and not send pupils home without having considered all the guidelines.
"All schools are different in terms of their pupils, staffing structures, size, buildings, open space, and local communities, so we have to trust in head teachers to make the right decision for their school, particularly as Covid rates vary significantly, even on a local scale.
"Unsurprisingly, parents have different viewpoints about school closure, partly because of their own family context. We need to support those who feel anxious.
"However, I have spoken to many parents in recent weeks and the overwhelming majority want their children in school but support the school if we need to send children home temporarily.
"I spoke to a parent of one of our more vulnerable pupils at the weekend and she is desperate for her child to return to school. To use her words 'He needs school'."
Sudden closures of schools, year groups or class 'bubbles' have caused problems for some parents, including greenkeeper Craig Simms of Northfleet who was at loggerheads with his employer when he was refused furlough to look after his daughters who had been sent home from school.
