Gerard Byrnes was eventually jailed in 2010 after pleading guilty to 44 counts of abusing 13 girls between 2007 and 2008.

School Principal Terence Hayes and student protection officer Catherine Long first heard a complaint from a schoolgirl, who said Byrnes touched her breast, in September 2007.

The Royal Commission into Institutional Responses to Child Sexual Abuse heard in Brisbane on Monday that during a meeting with the girl's father, Mr Hayes said he would deal with Byrnes internally.

But neither Mr Hayes nor Ms Long told police or parents about the allegation.

Ms Long said Byrnes regularly gave girls lollies and had them sit on his lap, and girls were "hanging off him" when he was on playground duty, but she thought he was just a popular teacher.

Meanwhile other parents began to find out that their daughters had been abused from police, who had been told by other victims.

A mother, known as KP, told the inquiry that after police swooped on Byrnes, the Catholic Education Office and the school denied any knowledge of allegations against him.

"I found out later, through media reports and court processes, that this was not even true - Mr Hayes was aware of complaints about Mr Byrnes for over a year but did not report them to police," KP told the inquiry by videolink.

"A report should have been made to the police straight after the first complaint was made to the school.

"If this had happened, KC (my daughter) and the other girls would not have been abused."

Another mother, known as KO, was told by police that her daughter, KA, had been abused by the Byrnes in 2008.

At KA's birthday party another girl told KA that she and her father had met with Mr Hayes and told him she had been abused by the teacher in 2007.

"Terry Hayes had told the family at the time the school would deal with it," KO told the inquiry via videolink.

"The family then moved to Brisbane not long after, so nobody else knew what Mr Byrnes was doing to the girls.

"We weren't warned or informed by the school."

Student protection officer Ms Long, who still works at the school, said she didn't think anyone was being abused because someone would have noticed and more girls would have made complaints.

"I don't get that our children, with all of the student protection and everything else we have, didn't have the courage to come forward," Ms Long told the inquiry.

"They didn't speak to us, the people they knew and trusted supposedly, they couldn't talk to their parents, and you heard their mums today, they still haven't spoken up.

"Why? What is it that's caused this, that's stopped these kids from speaking out? So I struggle with it."

The inquiry continues on Tuesday morning.