Parents of children at Trinity Academy Halifax, in Holmfield, have contacted the Courier to say students are being taken out of their normal lessons because they are wearing their PE shorts and T-shirts.
Some other schools in the borough have said children can come to school in their PE kits or non-uniform to help keep them cool during the sweltering heat being experienced today (Monday) and tomorrow.
The academy has said pupils can return to their lessons if their parents bring their usual uniform to school to change into.
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Louise Holt, whose daughter attends the academy, said: "I've had a meeting with the deputy head and I've brought her home as I didn't believe it was a reasonable sanction due to the weather.
"They have said they will allow no blazers. Ties can be removed in class but put back on whilst walking around the academy. Tights still to be worn regardless."
Another parent said: "I saw messages from others schools and just assumed it was across the board that they could wear their PE kits. It's not like he went in non-uniform, it's got the Trinity Academy logo."
Sarah Case, Principal at Trinity Academy Halifax, said: "The academy‘s uniform policy is clearly communicated and understood by students and parents however, due to the exceptional weather conditions, we have asked students to remove blazers and ties.
"Thin cotton shirts are much cooler whilst also maintaining professional standards.
"The conditions at the academy will continue to be monitored closely and if further uniform modifications are required this will be done and communicated to parents.
"There is a large hydration station in the centre of the building where students can fill water bottles with chilled water throughout the day and we are very fortunate to have a modern, light, and spacious building which is designed to regulate the temperature.
"A small number of students have chosen not to attend in academy uniform today; these students have been asked to work in the air-conditioned lecture theatre while their parents are contacted to ask them to bring their uniform in so that they can return to their normal lessons.
"As the forecast is for the peak temperatures to come after the end of the academy day (2.20pm), we have also made the decision that all after school clubs and all other student activities will be cancelled this evening to enable all students to return home before the peak heat of the day. Unfortunately, this includes the community litter picks which a number of our students and staff had signed up to."