Sweden's Prime Minister has branded an Islamic school 'disgusting' for segregating children as young as six by their gender.

An undercover video captured girls at a private Islamic school in Stockholm being directed to the back door of a school bus while boys used the front door.

The country's leader Stefan Lofven said Tuesday 'it does not belong in Sweden' to have primary schools dividing children, aged between 6 and 10, by gender.

Undercover video footage of girls being loaded onto the back of the bus and boys at the front

The issue was highlighted by the Kalla Fakta, or Cold Facts, program on Sweden's TV4 channel.

Al-Azhar school head master Roger Lindquist told Sweden's TT news agency that the school management was not aware of the division, but a journalist was reportedly chased off the premises while trying to question school officials about the issue.

Lofven's comments were mirrored by his education minister Gustav Fridolin, who called the practice 'completely unacceptable'.

'Obviously, we have weak rules,' he told the the Swedish Expressen.

'It is clear that we both need to tighten the curriculum to prevent mechanistic gender separation from taking place, and to strengthen the regulatory framework when it comes to denominational schools.'

Mr Lindquist told TT the segregation was a mistake and added: 'This is not something that has been known or sanctioned by school management.

'Both the principal and I note, after seeing the video, that it has happened, but it is of course nothing we support.

'It is important to point out that the staff is not driven by religion but a passion to work with cultural and integration issues.

'It is also important that the school is not based on Muslim values but democratic ones.'

The school held a press conference in reaction to the fall out and insisted Islam was taught as a separate subject.

It has previously been in hot water over separating gym classes due to a ban in Sweden on single-sex classrooms.