Fair Work Australia (FWA) has completed its inquiry on the alleged violations committed by former top-ranking officials of the Health Services Union (HSU) in Victoria but wrongdoings seen so far fell short of leading into a likely criminal case.

According to FWA general manager Bernadette O'Neill, the most that the three-year probe could come up were civil cases against four former HSU officers, all of whom she declined to identify.

In a statement issued on Wednesday, O'Neill said the subject officials in the investigation were found liable of violating rules embodied in the Registered Organisations Act, meaning FWA probers have appraised inconsistencies on financial management and record keeping when these HSU officers were still in office.

"In broad terms, the findings relate to the keeping and lodgement of required financial records and statements and general duties in relation to the financial management of an organisation registered under the Registered Organisations Act," O'Neill said in her statement.

The FWA report will be endorsed to the Federal Court for the appropriate civil remedy and most likely, the erring HSU officials will be made to pay fines of up to $2200, O'Neill said.

No further investigations will be made afterwards, she added, highlighting the absence of possible criminal proceedings to follow the controversy, which O'Neill clarified was separate from the inquiry being conducted on Labor MP Craig Thomson.

"I have decided that this action is in the public interest in part because of the deterrence effect and the need to maintain proper standard of conduct for organisations and their officials," O'Neill said.

No indication was given by the FWA if the Thomson probe would head the same way of the latest result.

Thomson, who served as HSU's national secretary prior to entering politics, has been the subject of FWA investigation for allegedly misusing corporate funds that were entrusted to him.

The Labor MP had denied the allegations and welcomed the FWA probe, which has been ongoing for more than four years now, prompting the Coalition to accuse that the government may be working to influence the whole process.

A criminal liability against Thomson could lead to his expulsion from the Parliament, a scenario that could disturb the balance of power in the government with the ruling Labor party holding only a precarious lead against the Liberals.

Yet Prime Minister Julia Gillard could heave a sigh of relief if Thomson would also end up facing only civil liabilities, which would ensure his continued stay in the Parliament, at least until after the next elections.

Opposition workplace relations spokesman Eric Abetz is hopeful that with one phase of the HSU probe all wrapped up, the FWA can now focus on its works on the Thomson case.

"Now that this minor aspect is out of the way, I don't think Fair Work Australia has any more excuses and they can now put all their resources into finalising the Thomson saga," Senator Abetz told ABC on Thursday.

Opposition Leader Tony Abbott is convinced that the slightest hint of criminal offence committed by Thomson could lead to the exit of the Labor MP.