Terrence Walker on Monday conceded his frank evidence at a corruption inquiry in Sydney would result in him being regarded as "a dog", a leper and potentially fuel reprisals.

The NSW Independent Commission Against Corruption is examining allegations prison officers used unwarranted force on an inmate at Lithgow Correctional Centre in February 2014 before deleting CCTV footage and planting drugs to justify a cell search.

The inquiry on Monday heard the victim, a bikie gang associate who can't be identified for legal reasons, abused officers on an intercom while complaining of not having a television in segregation.

In return, he received a visit from a specially-trained unit nicknamed "the ninja turtles" headed by Mr Walker, who recalled his instructions were to "put him in his place".

An official report said the inmate was injured when he tripped on furniture and landed on a toilet while trying to flush contraband.

"That report is all lies," Mr Walker told the inquiry.

He alleged colleagues colluded to fabricate a story after learning of the inmate's injuries, which included a black eye, bruising to the mouth and a rib injury.

"The term that was given to me at the time was that we had to clean this up because 'this one will come back to bite us on the arse'," Mr Walker said.

He alleged that comment was made by Brad Peebles, the then-manager of security who until weeks ago was an acting director and one of the most senior officials in Corrective Services NSW.

"It was clear what we'd done was wrong," Mr Walker said.

According to the official reports, the man's cell was searched based on a tip-off from a reliable source. A buprenorphine tablet (a methadone-like drug) was found but he was never charged.

Mr Walker alleged the tip-off was also a lie suggested by intel manager Brian McMurtrie.

Counsel assisting the inquiry Sam Duggan said the two-week inquiry would examine the culture and mindset of correctional officers with systemic corruption in mind.

"Importantly, it should not be assumed that the events which unfolded at Lithgow are necessarily isolated," Mr Duggan said.

"They are not."

Corrective Services NSW Commissioner Peter Severin said the department had co-operated fully with the probe.

"These allegations, if proven, represent completely unacceptable behaviour," he said in a statement.

A Corrective Services NSW spokeswoman said Mr Peebles had been "relieved from duty" for the course of the inquiry along with John O'Shea, the governor of the jail.

Mr McMurtrie is no longer employed by the department but the spokeswoman refused to provide the date of his departure or the circumstances surrounding it.

The inquiry before Commissioner Stephen Rushton SC continues.

Australian Associated Press