Civil proceedings against federal MP Craig Thomson should be postponed because it may cause a miscarriage of justice over the criminal charges he is facing, a court has been told.

Fair Work Australia is trying to push ahead with the civil case, arguing that matters in the lawsuit that do not overlap with the criminal proceedings should not be stayed.

Thomson's barrister Jim Pearce told the Federal Court on Thursday the entire civil proceedings should be stayed until the criminal matters had been dealt with.

He said the amount of publicity that the civil proceedings would attract, as well as their proximity to the criminal hearings, were reasons to stay the civil case.

Thomson would also face the burden of having to prepare for both sets of proceedings, he said.

If the civil case were to proceed, this could create a miscarriage of justice, said Mr Pearce.

"There is a possible miscarriage of justice due to the disclosure of defences which interrelate with the respondent's right to silence," he said.

Justice Christopher Jessup said Thomson would not be required to say anything about the circumstances constituting the criminal charges, if part of the civil case were to go ahead.

FWA alleges the former Labor MP misused union funds when he was the HSU national secretary between 2002 and 2007, using credit cards to spend thousands of dollars on personal expenses including prostitutes.

Thomson is also facing 154 criminal charges of fraud, alleged to have been committed while he was national secretary of the HSU.

He has vowed to fight the charges and will next appear in Melbourne Magistrates Court for a committal mention on May 22.

The Federal Court hearing continues.