"Pupils must be protected from all forms of fundamentalism," said Education Minister Jan Björklund to Dagens Nyheter.
Some Christian schools teach biology students that the world and the organisms on it were created by a supreme being. This is often presented as another valid scientific theory alongside evolution - something most scientists reject.
Religious Education will remain on the curriculum and it will still be allowed to start the school day with prayers. But in classes teachers will be expected to stick to the curriculum.
"End-of-term services in school are great," he said, and added that religious education would remain a school subject. But all elements of religious worship would have to be completely separate from class teaching.
Most independent schools in Sweden are privately owned but funded by government grants.
Björklund also said the Swedish National Agency for Education would double the number of inspections of both council-run and independent schools. He also announced a ban on anonymous financial donations to schools and said he would make it easier to close schools that were breaking the rules.
The stricter rules will be introduced in next year's education act.