About 120 pupils at a Staffordshire academy were taken out of classes and told to study at desks in a gym because they were wearing the wrong footwear.
The Hart School in Rugeley, Staffordshire, said the students had breached its "no trainers" rule.
It said its policy allowed only black leather shoes.
However, one parent told the Express and Star newspaper the school had enforced the rule only after parents had bought leather Converse shoes.
The parent said: "The school changed their policy at the start of the school year banning all leather Converse [footwear].
"Most parents had already bought these shoes beforehand and as they are not cheap have refused to change them, which has led to a high percentage of students being sent into isolation today.
"The majority of these students are missing vital revision time with their subject teachers."
About 20 students were taken home by their parents following the action on Monday.
'More than fair'
However the school, an academy which educates children aged from 11 to 18, said the rule was not new and it had sent three letters to parents to reinforce it this year.
"At the beginning of the school year, in September, all children were advised that if they were wearing the wrong type of footwear, they had until 30 September to rectify the problem," school spokeswoman said.
"By upholding a high standard of school uniform we are promoting the best behaviour and raising educational standards.
"All footwear must be plain back leather or look like leather and have no logo.
"Yes, the Converse shoes might be leather and black but they are, nonetheless, trainers. We feel we have been more than fair."