Schools that want to keep face mask requirements in classrooms after rules were scrapped in England this week will have to be personally approved by the education secretary.
Nadhim Zahawi told regional health chiefs that they would need to consult him on any plans to go against new national guidance that masks are no longer necessary in schools.
Dozens of headteachers around the country have told parents that their schools will continue to ask pupils to wear masks in class and in communal areas despite the national mandate being lifted on Thursday.
Schools North East (SNE), an education network in northeast England, said 80 per cent of schools in the region intended to keep some measures in place, including masks in classrooms and communal areas.
Chris Zarraga, director of SNE, said: “There are serious concerns for schools, with local pictures often radically different from the national picture.”
Andy Byers, head of a secondary school in Durham, encouraged his students to keep wearing masks in the coming weeks.
He said: “Case rates in the northeast are still relatively high. We currently have 60-plus students and 10 staff absent, having tested positive.
“Other local secondary schools are all in a similar position ... high levels of absence with some students missing important face-to-face teaching, and a reliance on supply teachers covering lessons.
“For this reason I would like to encourage students to continue wearing face coverings for the next two or three weeks until (hopefully) case numbers fall.”
Phil Randall, head of a secondary school in Exeter, told parents: “Despite the prime minister’s announcement earlier today regarding wearing of face masks in classrooms I will be requesting that students do wear them in classrooms as well as corridors in line with other local and national schools.”
He said the decision was influenced by a prediction by health authorities that Covid cases would increase in the area over coming weeks.
In a letter to MPs, Mr Zahawi said he would be consulted on any plans from local health chiefs to bring back face coverings in schools in areas with Covid outbreaks.
He said: “I met with directors of public health yesterday and we agreed that in the event of extraordinary outbreaks of Covid in localised areas, they will share their plans with me where they are recommending reintroducing face coverings in tightly-focused geographical zones, so that we can assess evidence and data to ensure any extra measures are proportionate.”
The government's decision on face masks in schools – announced on Wednesday along with an end to plan B restrictions – has been criticised as rash by some in the education field.
Dr Mary Bousted, joint general secretary of the National Education Union, said that while everyone wanted mask-wearing in schools to end ”when it is safe”, the latest move was ”premature“.
She said: “The danger is we lift restrictions too quickly before the effects of returning to school are clear.
“This will result in more education disruption which is extremely worrying particularly for pupils taking national exams this year whose education has been so badly disrupted already.”
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Additional reporting by PA
