The ruling by the SNP-Labour coalition follows emergency motions by Green councillors that allowed pupils to join climate protests with parental permission on two separate occasions earlier this year.
However, officials said the “potential for adverse risk to children who are absent and unsupervised is high and runs counter to child protection and raising attainment”.
Thousands of young people took part in school strikes at the Scottish Parliament building in March and May, with smaller groups protesting every Friday, as part of a wider UK movement in more than 100 towns and cities.
However, most headteachers were reported to be unhappy with councillors approving the absences.
An organiser for Scottish Youth Climate Strike (SYCS), which has planned more action for September 20 and 27, said the one-day limit sent the wrong signals.
“The climate crisis is the biggest threat to humanity, with the group most affected being the children,” said Dylan Hamilton, 15.
“All we want is a seat at the table with effective climate targets being decided. Allowing us to protest once a year is simply not acceptable and will not let us get across how serious this is to the people in power.”
Scottish Greens councillor Steve Burgess said it was right to expect routine attendance at school but a block on climate striking failed to put into perspective the relatively small time-off involved over the whole year.
He added: “Neither does it recognise the educational value of striking in developing young people’s social and political awareness, nor the fact that school climate strikes have been hugely influential in driving the global response to the climate emergency, particularly in Scotland. This is not the time to put up barriers against young people expressing fears for their future and being able to doing something about it.”