Two schoolboys were allegedly disciplined after refusing to kneel down and "pray to Allah" during a religious education lesson.
It was claimed that the boys, from a year seven class of 11 and 12-year-olds, were given detention after refusing to take part in a practical demonstration of how Allah is worshipped.
Yesterday parents accused the school of breaching their human rights by forcing them to take part in the exercise.
One, Sharon Luinen, said: "This isn't right, it's taking things too far. I understand that they have to learn about other religions. I can live with that but it is taking it a step too far to be punished because they wouldn't join in Muslim prayer.
"Making them pray to Allah, who isn't who they worship, is wrong and what got me is that they were told they were being disrespectful."
Another parent Karen Williams, 38, whose 12-year-old daughter is a classmate of the boys, said: "I am absolutely furious my daughter was made to take part in it and I don't find it acceptable.
"The teacher had gone into the class and made them watch a short film and then said 'we are now going out to pray to Allah'.
"Then two boys got detention and all the other children missed their refreshments' break."
She added: "Not only was it forced upon them, my daughter was told off for not doing it right.
"They'd never done it before and they were supposed to do it in another language."
She said the pupils were asked if they had water on them, and when one girl produced a bottle, the teacher began washing her feet with it.
Her husband Keith, 44, a painter and decorator, said: "The school is wonderful but this one teacher has made a major mistake. It seems to be happening throughout society. People think they can ride roughshod over our beliefs and the way we live."
The alleged incident, at the Alsager school, one of Cheshire's top performing schools, happened on Tuesday afternoon. The teacher, Alison Phillips, the school's subject leader in RE, is understood to be staying away from the school until the furore dies down, although she has not been suspended.
She is said to have got prayer mats out of the cupboard and also asked children to wear Islamic headdresses.
Deputy headmaster Keith Plant said: "I have spoken to the teacher and she has articulately given me her version of events."
Sources at the school said the incident could have been down to Miss Phillips instigating a role play and not properly briefing the pupils, all aged around 12, what she was doing.
A spokesman for Cheshire County Council said they were investigating. He added: "The headteacher contacted the authority immediately complaints were received. Enquiries are being made into the circumstances as a matter of urgency and all parents will be informed accordingly.
"Educating children in the beliefs of different faiths is part of Cheshire's diversity curriculum on the basis that knowledge is, of course, is essential to understanding.
"We accept that such teaching has to be conducted with commonsense and sensitivity."