All four centre-right parties in the opposition Alliance criticized the national school inspectorate's decision, and the education minister, Gustav Fridolin, said he shared their concern.
Separating boys and girls in primary school and lower secondary school “can not be a way of working with gender equality,” he told TV4 Nyheterna.
The minister said he would instruct officials on Monday to examine how to make changes to the existing legislation.
Nina Da Mata, a sports teacher at the Al-Azhar school, defended the policy and said she would teach in the same way in a non-Muslim school.
“The girls feel more secure when they are in a group of the their own,” she told Mivida, the Swedish Teachers Union newspaper.
The school was reported to the inspectorate by an individual who worried that gender-segregated gym classes risked perpetuating patriarchal norms.
But the inspectorate ruled that the quality of gym classes offered by the school did not differ between boys and girls.
The school’s principal told the inspectorate that the pupils had a “Muslim cultural background” and would not be able to participate in gym classes at all if boys and girls were in the same group.
The gym teacher Nina Da Mata elaborated:
“Some of our girls want to be able to take off their veils and wear shorts and T-shirts in their classes. The would be difficult if there were boys of the same age or a male teacher,” she told Mivida.
The former Minister for Upper Secondary Schools, Aida Hadzialic, said in June that Sweden needed to discuss whether to ban religious schools amid reports that some schools were segregating boys and girls.
Sweden's free school system of state-funded but privately run schools was introduced in 1992 and paved the way for religious organisations to operate schools as long as they stuck to the secular Swedish curriculum.