Simranjot Kaur, 13, and 11-year-old Prasimran Kaur, who are not related, study at St Anne's Catholic School in Southampton, Hampshire, were asked to remove their traditional religious headwear by headteacher Lyn Bourne.
Newly enrolled year seven student Prasimran was told to take it off shortly after walking into school, while Simranjot said a teacher spotted her outside the gates before lessons and asked her to remove her turban.
Both of the girls, who are baptised Khalsa Sikhs and take the mandatory female surname Kaur, refused to remove the headwear which can be worn by both sexes in their religion.
"I was forced to take my turban off after staff began unravelling it," said Simranjot, something which Sikhs regard as highly disrespectful.
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"It's discriminatory. They are a Catholic school and are supposed to support equality. There was a total lack of understanding. We need to change the school's policy," said Prasimran's sister Jaskiran, a former pupil.
"They are in the correct uniform the only thing different is the turban. If Muslims can wear hijabs then why can't Sikhs wear turbans?," said Simranjot's mother Sukhwinder Kaur.
"I would like to apologise to students and parents for any offence caused by our enforcement of our uniform policy this morning.
"The situation that occurred was a misunderstanding and I can confirm that both girls involved now have permission to wear a turban to school," head teacher Lyn Bourne said in a statement.
"It hasn't been a great first day back but I'm pleased the situation has been resolved. Southampton has a variety of diverse communities all of which recognise the need to be valued and respected," said Southampton City Council cabinet member for communities Satvir Kaur, a former headgirl there and a practicing Sikh.