In documents filed to the Federal Court, the Fair Work Ombudsman claims the university coerced and took adverse action against two casual academics.
They each had "anticipated hours" set out in their contracts, but ended up having to work more than expected.
When they complained, their supervisor in August 2020 allegedly said words to the effect of: "If you claim outside your contracted hours, don't expect work next year."
The university later decided not to offer one of the academics any further teaching work, after she claimed pay for additional hours and made a number of complaints or inquiries, the ombudsman alleges.
The regulator says those two actions amount to adverse action breaches, and it wants the university penalised for alleged contraventions of the Fair Work Act. The maximum penalty for each breach is $66,600.
In addition to the penalties, the regulator is seeking compensation for the two employees, one of whom still worked with the university's Melbourne Graduate School of Education when it launched the legal action.
"Adverse action and coercion directly undermine workplace laws and the ability of employees to exercise their lawful rights," Fair Work Ombudsman Sandra Parker said.
The ombudsman is conducting a separate investigation into casual academics' alleged underpayment at the University of Melbourne, and the National Tertiary Education Union says the latest legal action highlights deep problems with the sector.
The union says it consistently hears about similar allegations from other members, and that it is the fear of retribution that stops more people from coming forward.
"University governance is clearly rotten at the highest level, because wage theft just keeps happening on their watch," the union's Victorian assistant secretary Sarah Roberts said.
The university received notice of the legal proceedings overnight, a spokesperson said on Thursday, and it will look at the specific allegations carefully before responding through the relevant court processes.
The spokesperson said the university is committed to complying with all obligations to staff under the enterprise agreement, and values all casual employees.
"The university is currently working to identify any practices that are inconsistent with our obligations, and doing everything we can to make full remediation and ensure we fully comply," the spokesperson said.
"Separate to the legal matter at hand, the Vice-Chancellor last year apologised to past and current casual employees who had been paid less than they were due for work that they performed."
The union said the root of the underpayment issue in universities is the over-reliance on insecure work.
It is pushing for an 80 per cent secure work requirement by 2024 in its log of claims for a new enterprise agreement, which is under negotiation.
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