The return to secondary school in January will be staggered in England, with some starting online in rather than in class, the BBC has learned.
It will allow head teachers to set up a Covid testing scheme announced this week – but with exam-year pupils going back to start term as usual.
The National Education Union said making the announcement on the last day of the school term showed “panic”.
School leaders will be expected to run and manage the testing regime.
Secondary-school-age children have among the highest infection rates, but an official study suggests virus rates in schools reflect the levels in their local communities.
Virus rates have been growing fast in some areas, including London and south-east England, in recent weeks, with many schools affected.
The analysis of tests on 10,000 staff and pupils from Public Health England, Office for National Statistics and the London School of Hygeine and Tropical Medicine found 1.24% of pupils and 1.29% of staff tested positive for coronavirus in schools.
However, the impact of those cases will have been felt by many more, as close contacts were required to go home and self-isolate.
The government is insisting this is not an extension to the school holidays and primary schools will not be affected by the move.
But the move comes after the Department for Education instructed all local authorities to keep schools open in the final days of term, despite several initially telling parents that schools would close early and head teachers calling for more flexibility for online study.
Education Secretary Gavin Williamson is due to give more details later on Thursday.
But teaching unions are already angry that they will be required to train and deploy an “army of volunteers” to run the testing.
Joint general secretary of the NEU, Dr Mary Bousted, said: “Armed with a 30-minute training video they are being asked to administer tests to adolescents – who may have their own views about what is quite an invasive procedure.”
She added that contacting parents for permission to test itself was a huge task, let alone the schools running their own mini test, track and trace systems.
“Yet again ministers fail to understand the fundamental issues involved, and the effort and time it takes to operate Covid security procedures in schools.”