The Fair Work Commission will begin a fresh investigation into the Health Services Union in Victoria, after a complaint from the union's assistant secretary.

The investigation is new, and unrelated to issues surrounding former national secretary Craig Thomson's alleged misuse of HSU credit cards.

Fairfax Media last week reported that the Victorian union's assistant secretary and treasurer, Leonie Flynn, had complained to the Fair Work Commission, alleging ''cronyism'', the misuse of members' funds and Health Services Union resources being used for Labor Party preselection campaigns.

Fair Work Commission general manager Bernadette O'Neill (pictured) on Thursday issued a statement saying there would be an investigation as a result of the allegations.

Union secretary Diana Asmar released a statement on Thursday night to say the union would work with Fair Work to resolve any concerns it had with the union's processes.

Clay Lucas