Cardinal George Pell says a number of complaints of clergy abuse of children were wrongly dismissed.
"I don't have the statistics on that but too many of them certainly were dismissed and sometimes they were dismissed in absolutely scandalous circumstances," Cardinal Pell told the child abuse royal commission via videolink from Rome.
He said the tendency to dismiss complaints was more about protecting the church.
"At that stage, the instinct was more to protect the institution, the community of the church, from shame," he said.
"I'm not sure at that stage there was too much concern about protecting assets."
The cardinal, who was too ill to return to Australia for questioning, is testifying to the royal commission via videolink from the Hotel Quirinale in Rome in front of a group of survivors from Ballarat.
Under questioning, he said child sex abuse had been an issue for centuries.
"The church has made enormous mistakes and is working to remedy those but the church in many places, certainly in Australia, has mucked things up, has let people down," he said.
"I'm not here to defend the indefensible."
He said the church in Australia had put in place procedures 20 years ago, namely the Melbourne Response and Towards Healing.
He said the problems in the church was not down to a "few bad apples" or the structure of the church.
"I think the faults overwhelmingly have been more personal faults, personal failures rather than structures,"
"Let me remind you that the reforms in '96/ '97 occurred within the old structures."