THIRTEEN young Catholic girls were raped and molested by their teacher because five adults remained silent to protect the Church.

But the bishop they were trying to protect says he finds it "stunning" they didn't report the claims.

Principal Terry Hayes, assistant principal Megan Wagstaff, student protection officer Catherine Long and senior Catholic Education Office staff Chris Fry and Ian Hunter first heard pedophilia allegations against a Toowoomba primary school teacher Gerry Byrnes in September 2007.

None of them ever told police or parents.

The former bishop of Toowoomba, Bill Morris, who didn't hear about the abuse until after Byrnes' 2008 arrest, can't understand why all five failed to report him.

"It's stunning, I know. I can't get my head around it. Like I said to someone - well, we spoke about it recently. It's not rocket science," the bishop told the Royal Commission into Institutional Responses to Child Sexual Abuse on Monday.

The Catholic Church has proved it had a system on paper to report pedophilia, but witnesses have spoken of a more deeply ingrained culture of silence and protecting the Church.

"Do not compromise the bishop," was the motto of the diocese at the time, claimed Mr Hayes, Mr Fry and Mr Hunter.

Bishop Morris said Church culture was to not believe child sex abuse victims.

"Yes, and I think it may be, say, sometimes we've got to check out the story because you never know, they might be just making it up and we don't want to make a report on someone that's going to ruin the rest of their lives, I think that could possibly be part of it," he said.

Mr Hayes, who is still a teacher, has shouldered much of blame for Byrnes being left to abuse more children.

However evidence put to the commission's Brisbane hearings which wrapped up on Monday suggested the other four educators, and the Church itself, were also aware.

Byrnes was finally jailed for 10 years after pleading guilty to 44 child sex charges in 2010 and the Church has now paid over $3 million to nine of the 13 victims.

But for many victims the pain goes on - some girls have depression, others have become withdrawn, and at least one previously happy family has split up after the parents separated.

A mother, who can't be named, said if just one of the five adults had reported the abuse claims to police, the girls' lives would've been very different.

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

Bishop Morris, who was forced to resign by Pope Benedict XVI in 2011, believes the Church needs to change its ways or "we're going to be in real trouble."

But he also says the Royal Commission will help change the Church culture.

"It's a catalyst to get things right."

The hearings resume in Sydney on Wednesday.

Originally published as Silence condemned girls to pedophile