The return of most secondary pupils to school is to be delayed by at least a week to allow more time to introduce mass testing.
Education secretary Gavin Williamson told the House of Commons on Wednesday that the government must make an "immediate adjustment" to its plans to reopen all schools in January.
Secondary schools and colleges in some areas with very high rates of Covid infection rates will not open to all pupils in January, he added.
For those areas affected, face-to-face education will continue for only exam-year pupils, vulnerable children and children of critical workers.
In a statement, he said: "We must always act swiftly when circumstances change. The evidence about the new Covid variant and rising infection rates have required some immediate adjustment to our plans for the new term."
Earlier this month, the government said exam-year students would go back as normal on January 4 after the Christmas holidays, but the majority of secondary school pupils would start the term online to allow headteachers to roll out mass testing of children and staff.
It was expected that all pupils would be back in classrooms on January 11 however teaching unions had warned that allowing students to return put them at risk of catching the new variants of Covid-19.
Because the Covid infection rate is particularly high among secondary school age pupils, Mr Williamson said the government will now allow more time so every school is able to fully roll out testing for pupils and staff.
He said all pupils in exam years will now return during the week beginning on January 11, with all secondary and college pupils returning full-time on January 18.
During the first week of term after January 4, secondary schools and colleges will instead prepare to test as “many staff and students as possible” and will only be open to vulnerable children and children of key workers, he added.
He told MPs: "The latest study we have from Public Health England is that Covid infections among children are triggered by changes in the community rate.
“The study also says that the wider impact of school closures on children's development would be significant.
"I'm quite clear that we must continue to do all we can to keep children in school."
The education secretary said the "overwhelming majority" of primary schools will open as planned on January 4.
But he added that in a “small number of areas” where the infection rates are highest only vulnerable children and children of critical workers will attend face to face.
A list released by the Department for Education (DfE) included primary schools in most London boroughs as well as substantial parts of Essex and Kent, together with East Sussex and Hertfordshire, along with Milton Keynes, will be closed to all but a few eligible pupils.
The DfE said a list of “contingency framework” areas detailing which secondary schools and colleges would remain closed to pupils would be published before January 18.
For universities, including the University of East Anglia and Norwich University of the Arts, the courses where students are eligible to return in early January have been further restricted, prioritising medical and other courses where face-to face-teaching is necessary.
The wider return of students currently planned for the two-week period beginning January 25 will be kept “under review”. All university students should be offered two rapid tests when they return.
The announcement comes amid surging cases of the new Covid variant that has seen almost three quarters of people in England placed under Tier 4 restrictions.
Parents in Norfolk had expressed unease over the planned staggered schools return.
Commenting on today’s announcement, former Suffolk head Geoff Barton, general secretary of the ASCL head teachers' union, said: “The decision to further delay face-to-face teaching for secondary pupils is unsurprising in the light of rising Covid infection rates and the new strain of the virus, and seems sensible in these extreme circumstances.
“Nobody wants to see children out of school but the difficult balancing act between keeping education fully open and suppressing transmission of the virus has clearly swung in the direction of tackling the immediate public health crisis.
“However, we are concerned that the government is assuming that it will be business as normal for the majority of primary schools from the start of term.
“The government needs to urgently explain why it considers the full resumption of primary education to be safe in most areas despite alarming infection rates."
Jim Adams, chief executive of Clarion Academy Trust, which oversees Hobart High School in Loddon and Pakefield High, near Lowestoft, and joint chair of Educate Norfolk, said there remained “grave concerns” about the timing, the support available and the rushed timescale.
He said: “The DfE announcement regarding testing came in the last week of term. In effect, giving us 48 hours notice to set up from scratch fully functioning testing stations, capable of administering hundreds of tests a day.
“School leaders will have done what they can over Christmas, but to recruit and train staff in such a short time frame is challenging to say the least.”
Schools have had very limited guidance and we are largely working in the dark and having to second guess DfE announcements, he added.
“What is certain is that school leaders will move heaven and earth to do whatever they can to make their schools safe and to protect their communities.”
Binks Neate-Evans, executive principal at Evolution Academy Trust, which has primary schools in Norwich, had messaged parents to say that she was “unable give clarity to children staff and families about our schools following Gavin Williamson’s announcement, added it was “far from helpful for you and will do our best to seek clarity ASAP”.
Before the areas where primary schools are affected was revealed, she tweeted: “This is just not good enough for the families in our communities. They have to be able to plan, to talk to their employees/ers. It’s New Years Eve tomorrow!”
Dr Mary Bousted, joint general secretary of the National Education Union (NEU) said the Government had not published the scientific guidance on the risks involved in school and college reopening.
“This information is desperately needed - particularly as the new variants of the virus are 50pc more transmissible," she said.
“A longer period of online working for all primary, secondary and college students could suppress virus levels and buy time both for the roll out of the vaccine and to put in place measures that can keep schools safer.
“Uniquely school and college staff are being required to work in overcrowded buildings, with no effective social distancing, no PPE and inadequate ventilation.
“We would like Gavin Williamson to explain, if schools are not centres of transmission, why school age pupils are now the most infected age groups?”
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