The inquiry has the potential to terminate the careers of both men despite the seemingly minor nature of the complaints.

It also raises serious questions about the performance of the PIC itself, which has been regularly criticised by its own watchdog for being unfair and holding questionable public inquiries.

The PIC's investigation, believed to be codenamed Operation Alexia, has been prompted by three complaints made by a former NSW Police officer, Richard McDonald, who now lives   overseas.

He has alleged Mr Scipione misled the public and the NSW Parliament about the number of serving NSW Police officers with criminal convictions. and that Mr Scipione had "inappropriate discussions" in relation to the matter with  NSW Ombudsman Bruce Barbour.

He has also complained that Deputy Commissioner Kaldas "disclosed confidential information" to former NSW police officer Larry Cook who was in email contact with Mr Kaldas.

In response to questions put by the Herald on Friday, Mr Scipione said: "NSW Police cannot make comment on any PIC investigation."

Mr Kaldas responded simply: "I deny any wrongdoing."

Earlier this year,  complainant Mr McDonald found out under freedom of information laws that there were 437 serving NSW Police officers with criminal convictions.

At the time, Mr Scipione responded by saying: "In the majority of cases these officers will have been convicted of a low-range PCA or similar offence."

But when Mr McDonald obtained further details, Mr Scipione was found to be wrong, because serving officers had convictions for fraud, stealing, break and enter and serious assaults.

Most of those who had drink-driving convictions were in the mid to high range, offences that carry a jail term.

Mr McDonald initially complained to the NSW Police Professional Standards Command, which found the complaint was not sustained. A subsequent review by the Office of the Ombudsman on July 25 told Mr McDonald it agreed with the finding.

But on September 18, the PIC notified Mr McDonald by email that it had "taken over" the complaint.

Mr McDonald has subsequently provided the Herald with documents, including emails and correspondence from the PIC, NSW Police and the Office of the Ombudsman.

He said he had done so "in the interests of transparency".

While the PIC has refused to confirm or deny an inquiry is under way, Fairfax Media has learnt that Kieran Murphy, PIC manager of investigations, and Kym Modra, a senior PIC investigator, travelled to Thailand in mid-October to formally interview Mr McDonald.

A PIC computer expert also made the trip.

Mr McDonald told the Herald he was interviewed in Chiang Mai, where he now lives,  on several days and signed a record of interview a couple of days later.

This is supported by an email from PIC investigator Mr Modra, dated October 14, in which he details their travel arrangements.

Mr McDonald said the investigators were interested in emails between Mr Kaldas and Mr Cook, who are former colleagues.

The Herald has learnt that on Wednesday, three PIC investigators, including Mr Modra and an IT expert, turned up unannounced at Mr Cook's rural Queensland home.

"They had a warrant to look at my computer," Mr Cook told the Herald on Thursday.

"So I said sure, there is no communication in there that I am worried about. They basically said [they were looking at] the leaking of communications from police headquarters and that information had been supplied to me.

"I said there had not been any confidential information supplied to me."

He told the Herald that his email communications with Mr Kaldas had been "a personal discussion".

The emails, seen by the Herald, appear to be between Mr Kaldas and Mr Cook.

It seems Mr Cook forwarded them to Mr McDonald because the pair have also known each other many years, and the latter has subsequently provided the emails to the PIC and the Herald.

Mr Cook said the PIC investigators had also told him they were looking at the issues raised by Mr McDonald, of police with criminal records being allowed into the force.

"They said they were looking into the recruitment standards," he said.

On September 18 this year, the PIC sent Mr McDonald an email saying: "Please be advised that the commission has taken over investigation P1403249 from the NSW Police Force.

"The commission acknowledges that this complaint was based on information you communicated to the NSW Police Force. The commission will be in contact with you in due course in relation to its investigation."

Based on the visit by investigators to Mr Cook and what they told him, it appears the PIC is investigating at least two of Mr McDonald's complaints.

It's not clear whether they are looking at his complaint about Mr Scipione having "inappropriate discussions" with the Ombudsman, Mr Barbour.

Mr Scipione was questioned in Parliament by Greens MLC David Shoebridge on August 20 this year about a meeting with the Ombudsman.

Mr Shoebridge asked: "Did you not talk to the Ombudsman on 2 April about the complaint that had been made against you and was being investigated by the Ombudsman?"

The Commissioner replied: "Not about the complaint against me, no."

Trouble at the top of the police tree

The revelations come days after a parliamentary inquiry was established into a long-running police bugging scandal, which involves claims more than 100 officers – including Deputy Commissioner Kaldas – were illegally spied on by the force's Special Crime and Internal Affairs (SCIA) branch.

At the time of the illegal bugging operation more than a decade ago, Mr Scipione and another contender to succeed him, Deputy Commissioner Catherine Burn, worked in SCIA.

Sources have told Fairfax Media that since the scandal was made public three years ago, relations between the trio have become increasingly strained.

A secret Ombudsman's inquiry into the illegal bugging has caused concern because of the lack of transparency, prompting the establishment of the upper house parliamentary inquiry.

In supporting the inquiry, Greens MP and Justice spokesman David Shoebridge described the Ombudsman's "behind-closed-doors" inquiry as "causing real damage within the NSW Police Force".

"There are real concerns that high-ranking former and serving police, together with senior journalists, have been interrogated by the Ombudsman and forced into secrecy with the threat of criminal sanctions if they spoke out. This secrecy must stop."

Lives entwined within the force

Commissioner Andrew Scipione, APM

- Succeeded Ken Moroney as commissioner of the country's largest police force on August 31, 2007.

- Scipione's career began at the Australian Bureau of Customs in 1978 before moving to the NSW Police Force in 1980.

- He was seconded to the National Crime Authority of Australia in 1985, and spent time with Bankstown detectives, the Special Gaming Squad, Hurstville and Sydney City general duties.

- In 1998 he became the chief of staff to then police commissioner Peter Ryan, and in 2001 became the commander of Special Crime and Internal Affairs (SCIA). He became a deputy commissioner in 2002.

- His contract is due to expire in September 2015.

Deputy Commissioner Nick Kaldas

- Kaldas graduated from the Police Academy in 1981 and spent more than 10 years as a police hostage negotiator.

- He completed the FBI Hostage Negotiators Course in Quantico, Virginia, in 1996 and holds a Masters Degree in Public Policy and Administration.

- He has headed the state's homicide and gangs squads, and in 2004 was deployed to Iraq and became deputy chief police adviser. The following year he led the investigation into the assassination of Lebanese prime minister Rafic Hariri.

- He became an assistant commissioner (counter-terrorism and public-order management) before being promoted to deputy commissioner.

Richard McDonald

- Served as a NSW police officer from 1995-2003. He was suspended in 2000 for three years on full pay, before being dismissed in 2003.

- After a NSW Industrial Relations hearing, police agreed to reinstate McDonald, accept his resignation at the rank of senior constable and a confidential settlement was reached.

Larry Cook

- Joined the NSW Police in 1980 and left in 2003. He told Fairfax Media he knew Mr Kaldas from his policing days. Asked if he was a friend, he replied: "I am an admirer of Nick Kaldas for being an honest operational policeman."

- Mr Cook says he has no beef with individual investigators but he had no faith in the PIC.

- He says he was "let down" by PIC between 1999 and 2003 when he made complaints about corruption within the force's internal affairs branch, and describes the organisation as "politically driven".

The watchdog

The NSW Police Integrity Commission is headed by Police Integrity Commissioner Bruce James, QC, a former Supreme Court judge. In 2013-14, PIC received 1297 complaints of misconduct against both sworn and unsworn officers. They commenced a total of 177 investigations, 141 of which were just preliminary investigations.