Allegations that Health Services Union (HSU) whistleblower Kathy Jackson ran a secret fund worth $285,000 have been sent to the royal commission into union governance and corruption.

Craig McGregor, the secretary of the Victorian HSU number 3 branch, says an investigation of internal banking records has confirmed that large sums of money were transferred into an account called the National Health Development Account.

"We've referred this matter to the relevant authorities, being the royal commission of course, and to Fair Work," he said.

"I would think that something like this would need to be disclosed to the membership.

"In fact... there seems to be some suggestion that there were efforts taken to make sure that this information wasn't discovered."

Mr McGregor is not alleging Ms Jackson used the money to help her political allies get elected.

"I'm suggesting there was some untoward movement of money from the union to another account and as to what purpose that money was put, at this stage, we don't know," he said.

Nine HSU branches are holding elections in June and Mr McGregor was asked if he would be running against allies of Ms Jackson.

"Certainly one would expect in a robust union that there would be elections transpire in every branch, certainly," he said.

The development comes as Ms Jackson pursues a claim for back pay from the union.

"There's certainly some irony there," Mr McGregor said.

"Ms Jackson has had a very colourful presence in the media for a long period of time but I think to many on the inside this comes as no great surprise.

"It's been a frustrating period for a lot of people."

The ABC been unable to contact Ms Jackson for comment but in a statement to Fairfax, she declined to answer specific questions about the account.

In the broad statement, she denied using the money for her own private benefit or for payment to a third party unless she believed it served the legitimate political purposes of the union.

Ms Jackson gave evidence against former Labor MP Craig Thomson in his fraud trial and described the HSU as being like "being in a cult."