A survivor of clergy child sexual abuse has called on Catholic institutions in Melbourne to follow the lead of a Ballarat school, after it offered the first public apology to its abuse victims.

St Patricks College is one of Ballarat's most enduring Catholic institutions. Some students have graduated to become priests, archbishops and even a cardinal.

Cardinal George Pell was made school captain here in 1959.

But the school has also been the scene of trauma, violence and sexual abuse.

On Tuesday, at the foot of a red brick building which once housed the perpetrators, the school's headmaster acknowledged the harm.

"For abuse committed by religious and past staff of this college, on this site, abuse committed by religious who lived here and offended at other institutions within Ballarat and beyond, and abuse committed by ordained old collegians," John Crowley said.

"For childhood innocence lost; a time that should have been one of great wonder, that was stolen in the most despicable and heinous way, by the very people who are meant to protect and care for you, for this we apologise."

The father of a victim wept in the crowd, others stood silently with their eyes closed.

People will not forget

Survivor Keith Whelan was abused by convicted paedophile Edward Dowlan after the teacher was shifted from Ballarat to St Thomas More College at Nunawading.

Dowlan was convicted of 52 sexual abuse charges.

"Let's go to Melbourne now and hear it from Melbourne and all the rest of them," Mr Whelan said.

After the ceremony, the school opened a permanent garden dedicated to victims.

Survivor Andrew Collins said he understood that many victims would not have wanted to hear the apology.

"I hope that in time they come to see that, it's a start, the start of real change," he said.

"It's the most positive thing that I have seen happen in the last couple of years since the royal commission started.

"To have something here that's concrete, and not going to disappear — it means people won't forget, and that's very important."