Police were called to a school in Kent after hundreds of children walked out of lessons in protest over changes to the timetable.
Between 200 and 300 children are understood to have taken part in the protest at Dover Christ Church Academy.
Pupils said the protest was mainly about changes to the lunch hour, which meant they were split into two groups.
Head teacher Richard Williams said the pupils at the centre of the protest had later apologised to him.
Dover Christ Church opened as an academy less than a month ago.
Kent Police said officers were called to the school shortly before 1130 BST.
The school gate and three or four cars belonging to staff were all damaged.
The pupils later returned to their classrooms to await collection by their parents.
A police spokeswoman said two students who were already excluded from Dover Christ Church Academy were arrested, along with a 43-year-old man who was outside the gates.
The excluded students were arrested on suspicion of criminal damage and public order offences. The man was taken into custody on suspicion of common assault and a public order offence.
Mr Williams said in a statement the incident was "unfortunate for all concerned".
"The students at the centre of the protests contacted me this afternoon to apologise, recognising that the action of some of our students did not reflect their original intentions.
"Whilst we accept that some students might not support split lunch hours, it is a widely adopted practice in schools across the UK, not least because it allows for more efficient timetabling of classes and better management of the lunch break."
Dover Christ Church Academy is sponsored by Canterbury Christ Church University and Dover Boys and Girls Grammar Schools.
It is currently waiting to hear whether the school premises can be rebuilt.
A decision on whether the rebuilding of six Kent academies, including Dover Christ Church, can go ahead has been delayed until the results of the government's spending review.