The parents of a Perth boy with brain cancer have been ordered by Western Australia's Family Court to allow him to undergo potentially life-saving chemotherapy treatment.

Angela Kiszko and Adrian Strachan have said they do not want their son Oshin, 6, to suffer from the side effects of chemotherapy and radiotherapy.

A Princess Margaret Hospital (PMH) doctor took legal action after the parents refused to allow the treatment.

The Family Court Chief Judge Stephen Thackray said that while the parents tried to approach the matter on the basis of the best interests of their child, medical evidence could not be ignored.

In the decision, handed down last month, Chief Justice Thackray said parental power was to be exercised in the best interests of the child and was "not unlimited".

Chief Justice Thackray said the evidence was that Oshin would die within a few months if nothing was done.

He said there was a 30 per cent chance of survival at five years if he started chemotherapy immediately, and about a 50 per cent chance if he had chemotherapy and radiotherapy.

Those statistics from experts, he said, indicated a good prospect of a long-term cure.

AMA ethics committee supports treatment

National chairman of the AMA ethics committee Michael Gannon told 720 ABC Perth it was an extremely rare case.

"The doctor's responsibility is always to do the best for a patient, and when it comes to the care of a child, they need to consider the rights of the parent or guardian," he said.

Dr Gannon said it was standard practice for complex cases to be discussed by a multi-disciplinary team including a surgeon, oncologists and others.

"I have no doubt that a case like this would've been discussed extensively by the doctor in charge before they took the difficult and, I think, the very brave step of involving the courts," he said.

"It is very difficult to try and make the case to a parent or guardian that you think you know better than their wishes for their own child.

Dr Gannon said it was a vexed and difficult ethical issue.

"The burden of proof is very high, this is not something the doctors do commonly, it's not something that they would want to do," he said.

"The case of the medical evidence would have to be extremely strong before a judge would dream of going against the wishes of a parent or guardian."

The family's lawyer issued a statement saying they were continuing with full medical treatment for Oshin as directed by the medical staff at PMH and Sir Charles Gardiner Hospital.

It went on to say the family were "distraught and traumatised by the horrible condition their son is suffering".

In a statement issued late on Friday, PMH said the case was the first occasion in which the Family Court of Western Australia had made orders for the medical treatment of a child in circumstances where the parents had refused their consent for that treatment.

It said no further comment on the case would be provided.