The head of the state's healthcare watchdog told a royal commission its investigation into allegations about paedophile doctor John Rolleston was "indefensible".

Health Care Complaints Commission boss Kieran Pehm​ said the agency was beset by lengthy delays and poor information sharing at the time sex abuse claims about Rolleston were first received in the late 1990s.

In evidence before the Royal Commission into Institutional Responses to Child Sexual Abuse, Mr Pehm admitted  allegations about Rolleston were not investigated thoroughly and complainants were treated poorly.

"It's bad. It's indefensible," he said.

He told the royal commission that when he started at the HCCC in 2004, delays of two or three years were not uncommon and rhe ecalled there were 700 to 800 unallocated files piled up in a corner office.

The commission heard that when a sex abuse survivor, known as AWC, complained about Rolleston to the HCCC in 1998, it took almost a year for an investigation to commence.

Justice Peter McClellan​, who is presiding over the public hearing into healthcare providers and regulators, expressed surprise that Rolleston's failure to respond to HCCC investigators was provided as one reason for terminating the inquiry.

"If you have a complaint but you haven't had a response from the person complained about, that that is a reason to discontinue an investigation? It defies belief," he said.

"I agree," Mr Pehm replied.

The commission was told the historic nature of AWC's complaint was another reason for ending the inquiry in 2001, despite the fact Rolleston was still practising as a doctor.

When the HCCC received a fresh complaint about child sexual abuse involving Rolleston from another man in 2003, it failed to connect the new claim to AWC's case.

Mr Pehm blamed "poor information systems" at the time.

He agreed the response to Rolleston's victims was "completely inadequate" but said the HCCC had improved the time frames for investigations and simplified the process for complainants.

Rolleston was arrested in July 2009 and convicted of more than 30 sexual offences relating to adolescent patients he abused at his practices in St Ives, Whalan and at the Royal North Shore Hospital.

In earlier evidence, a senior medical practitioner who was molested by Rolleston as a child said he was stunned to learn his abuser was still allowed to practise while being investigated over sex offences.

The man, known as AWF, told the commission it was "incomprehensible" that healthcare regulators allowed Rolleston to continue to work as a doctor after allegations first surfaced.

The evidence before the commission is that Rolleston, who was imprisoned in 2011, was not deregistered until 2013.

"It seems to me that Rolleston could theoretically reapply for re-registration as a medical practitioner after four years, which is in May 2017, which I find troubling," he said.

AWC, who was molested by Rolleston at Royal North Shore Hospital in 1979, told the commission that the HCCC was

"completely ineffectual" in examining his report.

Mr Pehm is expected to continue to give evidence on Friday.

Adults Surviving Child Abuse: 1300 657 380 
Survivors and Mates Support Network: 02 8355 3711
Bravehearts: 1800 272 831