Thomson, 50, was on Monday found not guilty of 49 counts of obtaining a financial advantage by deception because a County Court judge found the prosecution's wording of the charges was incorrect.

However, judge Carolyn Douglas found Thomson guilty of 13 counts of theft, related to the withdrawals of cash from ATMs when he used Health Services Union credit cards for personal use, including paying for sex.

The court heard that between 2002 and 2007, when Thomson was the HSU national secretary, he spent about $5000 of union money on prostitutes and relocation expenses for when he and his then wife were preparing to move from Melbourne to the NSW central coast.

Defence counsel Greg James, QC, called for Thomson to serve a six-month suspended sentence, with no time in jail, given the former Labor MP for the NSW seat of Dobell had already been punished through the notoriety of his case.

Mr James said that at the time of Thomson's offending, he had travelled frequently yet was still serving the union's members.

He said paying for sex was "popularly unacceptable but not illegal".

Judge Douglas replied: "I don't care whether he went to a brothel or Bunnings. It's the breach of trust."

She said the amount of money he stole was not significant, but the breach of trust was "very, very serious" given his responsibility within the union.

Judge Douglas said she had thought Thomson "particularly lucky" when in March magistrate Charlie Rozencwajg imposed a penalty of three months in jail, with a further nine months suspended for two years.

Thomson never served a day of that jail term as his legal team launched an immediate appeal.

In ruling in Thomson's favour in the 49 fraud charges, Judge Douglas found the prosecution was wrong in alleging Thomson deceived credit card lenders, as was alleged in the charge sheets.

The judge said Thomson had deceived the HSU when he used the money, but that was not part of the criminal offence that was alleged.

"I find it regrettable the prosecution decided to charge the accused in such a way. That is an error that cannot be changed," she said.

Judge Douglas said she did not want her decision interpreted that she condoned Thomson's behaviour.

It was clear, she said, Thomson had used the credit cards to withdraw cash for his personal use, had no authority to do so and had previously drafted a policy on the guidelines for the use of union credit cards.

"But this is a court of the law, not of morals," she said.

Judge Douglas said there was enough evidence to prove beyond reasonable doubt that the cash Thomson withdrew from ATMs belonged to the HSU, and that he had no right to use it outside union purposes.

She found Thomson guilty on 13 charges of theft, but not guilty of two counts of theft because of insufficient evidence.

One other charge was withdrawn.

Thomson sat unmoved in the dock as the judge went through her reasons.

Thomson lost Dobell in last year's election while standing as an independent.

He is on bail as he awaits sentencing on Wednesday.