Research scientists at the Peter MacCallum cancer hospital did not receive millions of dollars owed to them in back pay, hospital financial records show, after a secretive $250,000 deal struck between the hospital and controversial union leader Kathy Jackson.

Ms Jackson has admitted using that $250,000 settlement as seed money for a bank account from which she withdrew tens of thousands of dollars and used for personal spending. at fashion boutiques and a pediatric dentist, and at David Jones, Gazman, JB Hi-Fi and Bunnings.

Ms Jackson, under oath, had claimed at the royal commission last month that workers received ‘‘millions of dollars’’ in back pay which she said was on top of the $250,000 payment made from the hospital in 2003 to her Health Services Union No.3 branch.

Detailed annual financial records from the hospital, obtained by Fairfax Media, show no record of any money being back-paid to workers nor the $250,000 settlement.

New evidence submitted to the royal commission will also allege that Ms Jackson actively discouraged hospital workers from pursuing the back-pay claim and warned them they could lose their jobs if they did.

Sources estimate the back-pay issue affected hundreds of staff over a number of years and estimate the hospital may have owed workers more than $2 million. The hospital did not answer questions and a spokeswoman said: ‘‘Peter Mac continues to undertake its own inquiries into the matter.’’

Ms Jackson, who sprung to national prominence as a corruption whistleblower at the HSU, denied wrongdoing and threatened to sue Fairfax Media. In an email to blogger and supporter Michael Smith she noted almost all the union's records were gone, possibly destroyed in a flood.

Ms Jackson said she told hospital staff it was "ok" for them to pursue their entitlements but many were concerned by cuts to operations if they did.

When the royal commission into the HSU resumes, the issue is expected to be examined closely and a senior official at the HSU, Rosemary Kelly, is seeking to challenge and cross-examine Ms Jackson on her evidence.

Dr Kelly will say a member of her No.4 branch told her that Ms Jackson in 2003 had discouraged research scientists at the hospital from pursuing back-pay claims, warning them they could lose their jobs if they did.

Dr Kelly, secretary of the branch that represents medical scientists, said she first discovered research scientists were being significantly underpaid in early 2003 when one of her members, about to start work in research, asked Dr Kelly to check what he should be paid.

She then told Ms Jackson about the under-payment issue as the workers affected were from Ms Jackson’s branch.

Legal advice from 2003 tendered at the royal commission by Ms Jackson also suggests workers were being told they may forgo their rights to back-pay.

The HSU advice notes that Ms Jackson’s branch, as part of the settlement, would not assist or encourage claims by members. It canvasses workers losing their rights to pursue the hospital for back pay if they agreed to support the settlement. ‘‘I consider that members signing the deed should presume that they will be thus prevented from bringing such a claim,’’ the advice said.

The national HSU is also seeking to cross-examine Ms Jackson at the royal commission and is separately suing her for $700,000 for misappropriation of funds. Part of that claim is to claw back the $250,000 from the Peter MacCallum settlement.

Ms Jackson was hailed by Tony Abbott and other senior Coalition figures for exposing corruption at the HSU. Her revelations contributed to the jailing of former national ALP president and HSU leader Michael Williamson.

But her credibility as a corruption ‘‘whistleblower’’ was called into serious question by a number of reports in Fairfax Media earlier this year and suffered further damage at the royal commission hearings.

Ms Jackson, at the hearings, was unable to explain a string of large withdrawals from her fund, the National Health Development Account, which was set up using the Peter MacCallum settlement money. When asked, she said she had no recollection of why large sums of money – ranging from $3500 to $50,000 – had been withdrawn as her only records were kept in an exercise book which had gone missing.

She said she had been authorised by her committee of management to spend $4000 a year for her personal benefit from the fund in lieu of overtime.

In her evidence to the royal commission, Ms Jackson contradicted a written statement from a member of her branch committee of management that workers did not get back pay.

‘‘A large number of members received a settlement in respect of their outstanding entitlements, but they also received a new structure and a new enterprise agreement that came out of that and security of employment,’’ she said.

‘‘They got their own settlement in respect of their outstanding entitlements.  There was millions of dollars at the time.''