La Trobe University has failed in its effort to qualify for JobKeeper after federal treasurer Josh Frydenberg clarified that Commonwealth funding is included in the turnover test for universities.
Almost two weeks ago, La Trobe cut non-essential casual positions due to the university facing financial difficulties during the coronavirus pandemic.
La Trobe vice chancellor John Dewar said it was the is second time the government had clarified JobKeeper eligibility exclude universities.
The clarification states that core Commonwealth Government financial assistance provided to universities will be included in the JobKeeper turnover tests.
"The first (change) was when the Government announced that a lower revenue downturn threshold of 15 per cent would apply to registered charities," he said.
"Since universities are registered charities, it was assumed that the lower threshold would also apply to universities. However, within 24 hours of that announcement, the Government 'clarified' that universities were still subject to the standard tests of 30 or 50 per cent.
"La Trobe, and the entire university sector, are facing an unprecedented crisis that could see 21,000 jobs lost, and put a $40 billion export industry at great risk. That the Federal Government would change their guidelines to exclude us again is very disheartening indeed."
JobKeeper payments provide staff in sectors heavily affected by coronavirus shutdowns with $1,500 per fortnight - the equivalent of about 70 per cent of the country's median wage.
Around 900,000 businesses expressed interest in the JobKeeper scheme before enrolments opened last week. So far more than 400,000 businesses have enrolled covering around 2.4 million employees.
Dr Dewar said missing out on JobKeeper eligibility meant La Trobe would miss almost $50 million in funding.
"(The clarification) means that we are no longer eligible for the scheme," he said. "The $50 million we hoped to receive in order to mitigate the impact of the current crisis on the jobs and livelihoods of our staff, will no longer be available to us.
"I am deeply disappointed by this. By applying for JobKeeper, we acted in good faith by following the published ATO guidelines.
"We obtained independent legal advice which unequivocally confirmed our eligibility for JobKeeper. We sought assistance under the scheme because we care about our staff."
Dr Dewar had encouraged La Trobe staff to apply for JobKeeper resulting in more than 3400 staff completing nomination forms.
"I am deeply grateful to all 3400 colleagues who took the trouble to complete the nomination form. I am truly sorry that it will not lead to the benefits we had hoped for," he said.
"We will continue to do everything we can to mitigate the impact of the current crisis on our staff."