Chief Commissioner Graham Ashton was head of the state's independent police watchdog when he learned the gangland barrister was a police informer.

Mr Ashton told a royal commission on Monday he would not have wanted to know because his job then was investigating misconduct and corruption in the force.

"Well here we are now more than 10 years later investigating just that," counsel assisting Chris Winneke QC retorted.

Ms Gobbo was a registered informer three times on and off between 1996 and 2009, ratting on clients including drug kingpin Tony Mokbel and underworld killer Carl Williams.

Mr Ashton admitted he might have learned more back then if he'd asked a few questions, but added matters involving sources were highly confidential.

Mr Ashton was also quizzed about his decision to stop using diaries while at the Office of Police Integrity in early 2006, a decision that came shortly before Mr Ashton may have learned Ms Gobbo was a police informer.

The chief commissioner claims he only learned Ms Gobbo was a police informer in July 2007 when she was called as a witness.

But it has also been claimed then chief commissioner Simon Overland told Mr Ashton in April 2006 so he could stop her being called in the secret hearings.

She had been scheduled to appear in 2006, but was withdrawn without explanation.

Mr Ashton was unable to say why on Monday, but rejected it was because Mr Overland had asked.

He also rejected that he had stopped making notes in his diary, following a meeting with senior police including Mr Overland, because of an agreement with the then-police chief.

Mr Ashton maintains while he knew about Ms Gobbo's informing earlier, he did not know the extent of her duplicity until 2011, when he ordered an internal investigation because of concerns around several ongoing court cases linked to Ms Gobbo.

The then-deputy commissioner did not notify prosecutors or defence lawyers in those cases, claiming he discharged his obligation by reporting it to his bosses.

Mr Ashton rejected Mr Winneke's suggestion there were attempts at "keeping a lid" on Ms Gobbo's snitching.

Several secret internal reports were ordered about Ms Gobbo, including one released earlier this year which revealed Mr Ashton once described the opportunity of having Ms Gobbo "potentially solve a bunch of ... murders or prevent others" as "this glittering prize" which could sometimes divert from the sensible steps that should have been taken.

He also defended officers linked to the scandal as doing their duty during the tough period of Melbourne's gangland wars.

"You're not seeking to excuse any behaviour ...?" Mr Winneke asked.

"No," Mr Ashton replied.

Australian Associated Press