Face coverings should be worn by secondary pupils and staff in local lockdown areas of England - such Bradford and Kirklees, after the Government made a U-turn.
The Department for Education (DfE) advised that face coverings should be worn when moving around corridors and communal areas.
They will not need to be worn in classrooms, because other protective measures will already be in place and they might affect learning, it added.
Face coverings will not be recommended in schools more widely, the department said, but added that schools will have the discretion to require them to be worn by staff and children in Year 7 and above in communal areas.
The change follows World Health Organisation (WHO) advice that children aged over 12 should wear masks, the Government said.
Just this week Education Secretary Gavin Williamson insisted measures being adopted by schools to limit the spread of coronavirus meant masks were not required.
But announcing the change in advice on Tuesday, he said: “Our priority is to get children back to school safely. At each stage we have listened to the latest medical and scientific advice.
“We have therefore decided to follow the World Health Organisation’s new advice. In local lockdown areas children in year 7 and above should wear face coverings in communal spaces.
“Outside of local lockdown areas face coverings won’t be required in schools, though schools will have the flexibility to introduce measures if they believe it is right in their specific circumstances.
“I hope these steps will provide parents, pupils and teachers with further reassurance.”
It comes a day after a Number 10 spokesman said there were no plans to review the guidance.
Full guidance has not yet been published, but is expected “shortly” the department said.
In a warning that advice could change again, the DfE said stricter guidance could be issued for schools nationally if the rate of transmission increases across the country.
Earlier Prime Minister Boris Johnson had hinted that guidance may change, as pressure grew on ministers from teaching unions and after Holyrood confirmed secondary school pupils in Scotland will be required to wear face coverings in between lessons, from Monday.
Mr Johnson told reporters the Government will “look at the changing medical evidence as we go on”, adding: “If we need to change the advice then of course we will.”
Mayor of London Sadiq Khan criticised the Conservatives for appearing only to make the decision following pressure.
He wrote on Twitter: “Our children must be able to return to school in a safe environment and I welcome the latest u-turn by the Govt – a step in the right direction.
“However, it is of huge concern that yet again the PM has had to be forced into following the advice of public health officials.”
Kate Green, Labour’s shadow education secretary, described the change as a “half baked U-turn”.
She said: “Parents and schools needed clarity and leadership, but instead the Government have just passed the buck back to them.
“Face coverings should be compulsory in communal areas in schools.
“Instead of this half baked U-turn the Government should have given clear guidance and a plan to deliver it.”
Geoff Barton, general secretary of the Association of School and College Leaders, which had called on the Government to keep its advice under review, said the change was “inevitable”.
He said: “The new policy is discretionary, other than in places where coronavirus restrictions apply, and secondary school and college leaders will welcome the flexibility this affords them to decide what best suits their circumstances.
“We look forward to seeing the full guidance as early as possible.”
Post-primary pupils in Northern Ireland will be asked to wear face coverings in corridors and other communal areas, Stormont’s education minister Peter Weir said on Tuesday.
The official guidance comes into effect on August 31 when schools there return on a full-time basis.
Welsh health minister Vaughan Gething said a decision on schoolchildren wearing face coverings will be made on Wednesday, but current guidance says masks are not being recommended.
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