Victoria's Supreme Court has found in favour of former police chief commissioner Christine Nixon, who was being sued by the former secretary of the Police Association for an alleged malicious prosecution.

In a lengthy trial, Paul Mullett claimed Ms Nixon and two other officers had him charged with crimes that were never fully investigated as part of a campaign to have him sacked.

Mr Mullett was suspended from Victoria Police in 2007 before being charged with perjury and attempting to pervert the course of justice.

The charges were later dropped.

Ms Nixon, former deputy commissioner Keiran Walshe and Superintendent Wayne Taylor were also cleared of allegations of misfeasance in public office.

Supreme Court judge Terry Forrest found in the group's favour and cleared them of any wrongdoing.

"I have found that Ms Nixon had a sound motive for wanting Mr Mullett removed from his position at TPA [The Police Association] – he was a fierce adversary," Judge Forrest said.

"The existence of this motive, however, simply does not prove that it actuated Mr Mullett's subsequent suspensions and prosecution.

"I am positively satisfied that it did not."

Ms Nixon welcomed the decision and said she hoped the matter was over.

"This matter's now gone on for nearly four years and it relates to incidents that happened back in 2007," she told 774 ABC Melbourne.

"I was really pleased to get the decision today."

"To have the accusation and then to have it in the media and then to have various people suggest to me that I might have behaved inappropriately during this whole last four years, I think it is a disgrace."

Reputation tarnished in long-running matter, Ms Nixon says

Ms Nixon said the case had tarnished her reputation.

"I think as the court case proceeded we were able to see there was no substantial evidence there," she said.

She said she did not know whether Mr Mullett would appeal.

Ms Nixon also questioned the decision of the United Firefighters Union — currently embroiled in a bitter enterprise bargaining dispute with the CFA — to support Mr Mullett to proceed with his case.

"I feel sorry for Mr Mullett, I wish he'd got on with his life," she said.

"Nine years after this incident he's still pursuing me through the courts and I think he's been able to do that because he's been funded to do that.

"I think [the UFU] is an organisation now that I wonder about some of their behaviours."

UFU secretary Peter Marshall has separately been accused of bullying former emergency services minister Jane Garrett.

Mr Mullett did not make any comment as he left court.