Michelle Mulvihill, who dealt with more than 120 of the order's child abuse victims during compensation negotiations, claims Cardinal George Pell was aware of a loan by the Catholic Church to the order, which was later used by the order to pay victims of abuse.
She also alleges the order has never properly supervised suspected paedophile Brothers and has hid documents relating to the abuse in places where police ''would never find them''.
Dr Mulvihill's revelation came as the former prime minister Malcolm Fraser joined the independent MP Tony Windsor and the senator Nick Xenophon in calling for a national royal commission into sexual abuse by religious groups and other institutions, after claims by Detective Chief Inspector Peter Fox last week that the church was still covering up the crime.
Mr Fraser said the church should have nothing to fear from a royal commission if it had nothing to hide. ''Isn't it time we laid the issue at rest and made sure that all the institutions in Australia have procedures in place that will protect children?'' he said.
A spokesman for Cardinal Pell last night confirmed he had supported the payment of a loan to the order because the order had a liquidity problem. ''It is not possible to confirm the details today,'' the spokesman said.
The spokesman denied the cardinal was involved in any investigation of any abuse within the order. He said the cardinal was not briefed on any outcomes.
Up to 200 victims have sought compensation from the St John of God order after alleging they had been abused in special schools and homes run by the brothers in NSW, Victoria and New Zealand.
Last week a Melbourne inquiry into child abuse heard allegations that Brothers had drugged and pack-raped boys at their operations in Victoria.
Claims were also made that two boys had allegedly been beaten so badly they were thought to have died but their deaths had not been reported to authorities.
And Fairfax Media has obtained documents revealing that in the 1960s and 1970s dozens of boys were brutally assaulted at Kendall Grange, the order's school for mentally and physically impaired boys at Morisset on the NSW central coast.
Dr Mulvihill, who is based in Sydney, worked with the order for nine years from 1998, sitting in on meetings involving negotiators from the order and 150 victims in NSW, Victoria and New Zealand.
But she says she quit the job in 2007, fearing that suspected paedophile Brothers still wielded too much power in the order and were interfering with victims' compensation and treatment.
On Sunday she described the order as hosting Brothers who were responsible for "the worst examples of child abuse I have ever heard of" and said of the 40 to 50 Brothers who had been in the order around the time she was involved, about 75 per cent had been the subject of allegations.
"There was a small gene pool as to who you could talk to [about the abuse],'' she said.
She also alleged the church and now Cardinal Pell had been well aware of the extraordinary numbers of victims as the order's head, Provincial Peter Burke, had borrowed millions of dollars from the church to pay victims in a deal overseen by Cardinal Pell.
Cardinal Pell's spokesman said the order was not responsible to any Australian bishop. It managed its own affairs and reported to its headquarters in Rome.
''Cardinal Pell was not involved in the investigation of any abuse within the order. He was not briefed on any outcomes. He was not involved in the payment of any 'hush money' … Cardinal Pell's recollection is that the order had a liquidity problem in meeting its obligations to victims, that a loan was made by the Sydney Development Fund and repaid.''
Cardinal Pell supported this.
Dr Mulvihill said that last year she had given a statement to NSW Police investigating the order's operations at Kendall Grange.
She said she believed documents had been placed in special hiding places where the police would never have found them - locations known only to a few people.
''They are in spaces on Brothers' premises that are extremely hard to find. There's only a couple of people who know where they are.''
The order would not comment.