Former federal MP and Health Services Union figure Craig Thomson will not return to a civil trial against him after leaving a Melbourne court to see his psychologist and ward off the risk of suicide.

The Fair Work Commission is suing Mr Thomson for alleged misspending of HSU money when he was national secretary between 2002 and 2007.

The trial had been due to begin this morning but Mr Thomson made an interlocutory application to have it thrown out, saying he was too mentally unwell for it to proceed.

The court refused his application.

After the ruling Mr Thomson said he was too mentally unwell to continue and needed to see his psychologist.

Speaking outside court, Mr Thomson became emotional.

"To make that sort of application and then have it totally disregarded, I think is an unfortunate thing for the Federal Court," he said.

"I would hope that they would deal with mental health issues in a more compassionate and understanding way in the future.

"Otherwise these sorts of issues will never be raised because of the personal costs in terms of raising them."

Mr Thomson said he would return home to the NSW Central Coast immediately.

"I have decided today on the advice of my health practitioners that if the judge wants to continue the case, I'm at risk of not being able to conduct that case and degenerating into a stage where I may take my own life," he said.

"That is something I'm not prepared to do."

Justice Jessup had earlier questioned why Mr Thomson had left his application so late.

In response, Mr Thomson said he had been caught up with his prior criminal matters and had been struggling mentally.

The case continues this afternoon.

Civil case follows criminal trial

The civil trial follows a lengthy criminal trial in the Melbourne Magistrates Court in which Mr Thomson was jailed for inappropriate use of his union credit card on expenditures such as escorts.

He appealed the sentence immediately and was released on bail.

An appeal in the Victorian County Court acquitted Mr Thomson of the majority of charges last December.

He was found guilty of 13 theft offences.

Mr Thomson previously told the Federal Court he could not afford a lawyer for this latest legal challenge and would be representing himself for the civil trial.

He earlier told the court the Fair Work case against him should not proceed on the grounds his life was a day-by-day prospect and he had been punished enough.

"I wish I wasn't here making this submission ... I wish I was here represented," Mr Thomson said. "But I'm not."

Mr Thomson told Justice Christopher Jessup that "unlike most people" he was having to "weigh up my future" every day.

"That is a daily consideration ... whether I should continue in my life," he said.

"My wife won't leave me home alone ... she's concerned I might kill myself.

"I'm not capable in a mental health sense to run this case ... for what punishment could be greater than what I have already gone through in the last six years.

"If you want to have a very tight legal structure and avoid the truth, that's up to you."

Mr Thomson said he was "up against" an organisation (the HSU) that had already spent in excess of $2 million pursuing him.

He also described the Fair Work Commission as inefficient and incompetent.

"Justice delayed is justice denied, Your Honour," he said.

Media 'harassment' contributed to poor mental health

Mr Thomson told the court he had been subjected to a "hostile parliamentary environment" while a federal MP for the seat of Dobell and had been harassed by the media.

Mr Thomson submitted a collection of media articles he said had contributed to his state of mind, and went through them one by one.

They included articles on the ABC's The Drum website and by the Australian Associated Press.

Mr Thomson said the media camp at his central coast property in recent years and harassment of his wife Zoe was "entirely relevant to the effect on my mental health".

Mr Thomson also claimed the description of his vote in Parliament as "tainted" by the now-Prime Minister Tony Abbott and other federal MPs had upset him.

He also said Coalition frontbenchers George Brandis and Barnaby Joyce had flown to the wedding of "shock-jock Michael Smith" where he was talked about and humiliated.

Justice Jessup told Mr Thomson he could "understand" what he was saying and he did not need to underline the effect the last few years had had on him at "an ordinary person level".

But he said an expert, or lawyer, making statements before the court "would be required to set out the primary facts and evidence".

Justice Jessup earlier told Mr Thomson that Parliament was hostile by its very nature.

"You can't expect Parliament to be nice," Justice Jessup said.