The Swedish National Agency for Education has withdrawn the licence of Manar Al-Houda school in Uppsala because it was not following the national curriculum.
The school's leaders claim that they had made all the necessary changes and that the decision was political - coming after stories in the national media have fuelled public fears that Muslim schools are hotbeds of fanaticism.
The agency says it revoked the licence because the school had not rectified flaws identified by inspectors last year.
Manar Al-Houda is appealing against the decision, which will lead to its closure. No appeal case has ever been won.
The school was first rebuked last year after an inspection found that pupils did not receive an education "comparable to that provided by a state school".
Inspectors said the school paid more attention to parents' wishes than to national guidelines and that the teaching of Swedish was insufficient. They also found pupils, of no matter what background, were forced to follow Arabic for native speakers and study only Islam in religion classes.
The agency also criticised the methods for dealing with bullying and to help students in need of special support.
The school's reputation was damaged when a television programme showed one of the teachers allegedly physically bullying pupils in class. Police were notified but no charges were brought.
Claes-Goran Aggebo, a spokesperson for the national agency, said: "Pupils have not received the education they're legally entitled to."
Rumours persist, however, that the agency's decision was politically motivated, given the growing concern that independent religious schools are straying too far from the national curriculum. This has been fuelled by suggestions on national radio that wealthy Saudi fundamentalists are buying influence in Sweden's Muslim schools and immigrant community organisations.
Khaled Wafai, principal of Manar al-Houda, said: We've brought religious education back into line with the national curriculum. We were criticised for lack of music teaching. We've sorted that. Is it because we're a Muslim school? We just don't understand what the problem is."
Ingela Nordh, a senior teacher, said she was "astonished" because the school had rectified the problems identified last spring.
Mrs Malak Houssami, who has two children at the school, said: "It seems this is really about religion. If it's possible to shut down a school on these grounds, then many schools in Uppsala would be shut down."