The reported rape of a six-year-old girl in state care was categorised as "minor" by an initial investigator, South Australia's Child Protection Systems Royal Commission has heard.

The inquiry, sitting in Adelaide, was prompted by the case of paedophile Families SA carer Shannon McCoole, who is now in jail for sexually abusing young children in his care.

It is currently examining an internal investigation that happened after McCoole was suspended from duty.

A work colleague said she rushed into a room after what sounded like McCoole climbing onto a bed while tucking a six-year-old girl in.

The woman said she heard McCoole whispering, then the child saying: "Stop, don't tickle me there" and witnessed the girl on all-fours with a look of "sheer terror".

A former investigative manager with the Education Department, Catherine Harman, initially assessed the reported concern and said she classified it as "minor" because there had been no disclosure from the child.

"I thought we were in a roadblock and we needed more information," she told the inquiry.

"There was always a level of discomfort about what was heard."

Ms Harman spoke of a big number of matters usually requiring investigation but denied she gave the report a low priority rating because of it being "too hard" to deal with.

The royal commission heard McCoole was not interviewed until a later stage and denied the allegations, but was not pressed to explain the reported observations of his work colleague.

Given clearance to return to work, he was then arrested the following year as part of a global police investigation of a child abuse website.

Social worker interviewed child in public setting

Social worker Toni Jezeph was asked to interview the girl about whom the report had been lodged and told the inquiry her supervisor had spoken of the case as having "nothing in it" as a staff personality clash seemed to be involved.

Ms Jezeph said the senior staff member told her McCoole was loud and some people were unsure how to cope with that but, of the allegations, said: "There's no way he would do that."

PHOTO Toni Jezeph admitted, in hindsight, she could have handled her investigation better.

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Counsel assisting the royal commission Emily Telfer asked Ms Jezeph: "What impression were you left with about how seriously [the case] was being perceived?"

The social worker responded: "I actually didn't think it was very serious at all by that stage."

Ms Jezeph said she was told not to ask the child any leading questions, and interviewed her in a dining room while other people were present and as the girl played with an electronic game.

Ms Telfer questioned Ms Jezeph about the setting involved.

"Do you agree that talking to a child about something as weighty as potentially being sexually abused required some privacy?" she asked the witness.

"Well, as I said, hindsight is a wonderful thing but I suspect I was swayed by the stuff I'd been told about beforehand," Ms Jezeph responded.

She denied she had not taken the interview seriously enough at the time.

"I just went based on what I was told, whether it seems thorough or not — obviously now it doesn't — but at the time I thought I was doing the right thing," Ms Jezeph said.

"I listened to what people told me and that was probably my mistake."

The inquiry continues.