The New South Wales policeman who blew the whistle on an alleged cover-up of child sexual abuse in the Hunter Valley says senior police searched his office for sensitive files while he was on leave.

The inquiry is looking at how complaints about deceased former priests Denis McAlinden and Jim Fletcher in the Maitland-Newcastle diocese were investigated.

It was sparked by the allegations of whistleblower Detective Chief Inspector Peter Fox, who is giving evidence today.

Peter Fox has told the inquiry two senior police officers turned his office upside down while he was on leave for a month.

He said the sensitive files they were after were in a secure safe, but after that he started to distrust senior police.

Earlier, Peter Fox told the hearing that a statement from a victim of James Fletcher was the most difficult he had taken.

"The crimes were of the most horrid nature, the worst I've heard," he said.

Detective Chief Inspector Fox told the inquiry there was collusion by the then Bishop Michael Malone as well as other clergy.

He said James Fletcher was warned by the church he was being investigated in June 2002.

Detective Chief Inspector Fox said that gave Fletcher full knowledge there was a complainant and who that complainant was, and gave him the opportunity to destroy evidence that would have affected the investigation.

He also told the court, he has heard a former policeman Troy Grant describe other officers aligned to the church as the "Catholic mafia".

Detective Chief Inspector Fox said Mr Grant's investigation into another paedophile priest Vincent Ryan was hindered when he was continually given other substantial cases to investigate and sent away on trips.

He said Mr Grant was not able to fully investigate the case, and it felt deliberate.

New South Wales Deputy Senior Crown Prosecutor Margaret Cunneen SC is overseeing the inquiry.

In her opening address, she told the inquiry that children are "vulnerable and innocent" and that sexual abuse "casts a shadow over their whole lives."

The Commissioner said all sexual abuse is a gross and inexcusable breach of trust.

"The diocese of Maitland-Newcastle has had a very troubled history regarding issues of child protection and the sexual abuse of children," she said.

The Commissioner said it is not too late for victims to come forward.

"I have previously encouraged and continue to encourage these people to contact the inquiry so that their voices may be heard," she said.

Hunter Valley man Peter Gogarty was abused by Fletcher when he was a boy.

Before the inquiry, he said he hopes anyone found to be involved in a cover-up will be brought to account.

"I think a prosecution out of this, of senior people in the Catholic Church would be a wonderful outcome for the victims," he said.

"I will be very, very interested to find out if the police have deliberately decided that it was too hard to investigate these matters, then that's a serious, serious concern for our community."

He said he was very happy the inquiry was going ahead.

Over the next two weeks, the inquiry will hear from eighteen witnesses, including some of the state's most senior police officers.