The South Australian Education Department is being sued by a student and her father over allegedly failing to meet its Duty of Care in relation to a sexual assault.

According to the ABC, documents filed in the Adelaide District Court claim the girl was punched, kicked and sexually assaulted in an Adelaide Hills primary school toilet cubicle by another student.

The documents said the victim moved schools after the alleged perpetrator returned to the school after being suspended.

"The principal ... proposed that both (girls) continue to attend the school, despite continual objections and concerns voiced by (the alleged victim's) parents," the claim said.

"The [Department] owed the plaintiffs a duty of care to take reasonable care to ensure the safety and welfare of the first plaintiff whilst she was a student at one of the schools under its control and it was reasonably foreseeable that if it failed to meet its duty of care the first and second plaintiffs may suffer injury, loss or damage."

Both the girl and her father claim they now suffer from depression and each want up to $50,000 in compensation, as well as damages.

The Education Department has denied the claim.

"Any action taken was in accordance with Department policies and the Education Regulations 1997 (SA)."

It said the alleged perpetrator denied the assault and "in all the circumstances the [Education Department] acted at all times in a reasonable manner".