Teachers and headteachers criticised the government for "last-minute" guidance on what to do during virus outbreaks and local lockdowns as guidance for England was published just days before many schools began term.
The NAHT school leaders' union said the timing was "reprehensible".
In local lockdowns, secondary pupils could be kept home every other fortnight and, in an outbreak, large groups could be told to self-isolate.
Paul Whiteman, general secretary of the NAHT, said the decision to publish the guidance just before a bank holiday was "nothing short of reprehensible and demonstrates a complete lack of regard for the well-being of school leaders and their teams".
The guidance says this would only happen after "all other measures have been exhausted" - but if cases continue increasing, all students might have to move to remote learning apart from those in vulnerable groups.
Education Secretary Gavin Williamson said the document was a contingency plan for a "worst-case scenario".
Health protection teams will advise schools how many pupils need to isolate for 14 days.