The Christian Brothers who ran children's homes in Western Australia in the 1940s, 50s and 60s did not consider the abuse of students a crime, a royal commission has heard.

Brother Anthony Shanahan, a former province leader of the Christian Brothers in WA, today gave evidence at the Royal Commission into Institutional Responses to Child Sexual Abuse in Perth.

The inquiry is examining alleged sexual and physical abuse in four homes run by the Brothers in Perth, Tardun and Bindoon between 1947 and 1968.

Brother Shanahan told the hearing the mindset at the time meant abuse was not thought of "first and foremost" as a crime, but as a moral fault or failing.

"I think they saw it as something that was abhorrent, harmful - although I don't think they understood it as harmful in the way we would now, in terms of consequences for the victim, but something that was abhorrent and harmful and that was the way they dealt with it," he said.

The chair of the commission, Justice Peter McClellan, described the attitude as "somewhat extraordinary".

Brother Shanahan said brothers who had been accused of abusing students at boarding houses were often sent to day schools.

Brother Shanahan also told the hearing one of the rules laid out in the Brothers' constitution from 1962 stated that they were prevented from developing particular friendships with their students or fondling them.

He said a brother accused of fondling a boy might receive a warning and be transferred from a boarding house to a day school where it was thought there might be "less opportunity for misconduct".

When asked by Justice McLellan whether it was wise for brothers who abused children to be moved to another facility where children were present, Brother Shanahan answered "no".

Brother Shanahan told the hearing that between 1947 and 1968 there were no written policies relating to child protection, the handling of abuse complaints or the disciplining of alleged offenders.

He said a complaints process was developed in the 1990s as the order became aware of allegations.

The commission has heard four brothers accused of abusing boys in WA were the subject of charges, but only one was jailed.

WA's Deputy Director of Public Prosecutions (DPP), Bruno Fiannaca SC, told the hearing that state law in the 1990s struggled to respond to child sexual offences.

Mr Fiannaca said the law at the time made it difficult to join a number of complaints made by different people on the same indictment.

He said improvements have since been made and the DPP is now more likely to get a conviction.

"I think the law as it applied back in the early 1990s certainly struggled for reasons I've outlined in my statement, decisions of the High Court in particular," he said.

Recommendations on historic sexual offences

Justice McLellan has flagged that he will make recommendations aimed at making it easier to prosecute historic offences.

He said the issue of historic offences had divided judges and the High Court.

"The law has struggled very much to come up with a clear answer to the problems, and I guess the royal commission will have to take on that struggle head on," he said.

"We will try and resolve the best situation and provide a model for the whole of Australia, but whether we succeed is another matter, but that's what we'll try and do."

This morning's proceedings were delayed when a man had to be ejected from the hearing room after yelling at the commissioners, accusing them of a cover-up.

Justice McLellan asked the man to be quiet and he was removed a short time later.

The hearings continue.