The author of a damning and lengthy report into the Health Services Union (HSU) and now-suspended Labor MP Craig Thomson has retired from the public service.

Investigator Terry Nassios conducted a three-year probe before reporting on alleged irregularities within the HSU for Fair Work Australia (FWA), now known as the Fair Work Commission (FWC).

Mr Nassios was criticised for the time it took to conduct the investigation, which identified instances of union officials using members' funds for escort services and cash advances.

In a review undertaken last year, business advisory group KPMG, said the investigation had taken too long.

FWC general manager Bernadette O'Neill told a Senate estimates hearing on Wednesday that Mr Nassios retired on February 1.

Opposition workplace relations spokesman Eric Abetz, who had questioned Mr Nassios in previous estimates hearings, wished him the best for his retirement.

Education, Employment and Workplace Relations standing committee chair Gavin Marshall said Mr Nassios had faced difficult rounds of questioning during his previous estimates appearances.

"It was a difficult time for him," the Labor senator said.

"Some of that criticism was unfair and unfounded."

Mr Nassios had presented himself with dignity, Senator Marshall said.

The investigation report alleged 156 contraventions of union rules and workplace law by Mr Thomson when he worked at the union.

He has since denied any wrongdoing and has previously labelled the FWA report biased and selective.

Mr Thomson later faced civil proceedings brought by FWA but these were adjourned on February 1 pending separate criminal proceedings.

The NSW MP, who now sits in parliament as an independent, was later charged with 154 counts of fraud alleged to have been committed between 2002 and 2008 and when he was HSU national secretary.

FWA changed its name to the FWC on January 1.