Victorian Ombudsman Deborah Glass said thousands of Victorians were unjustly and inhumanely denied a COVID-19 border exemption to return from NSW to farewell dying loved ones, get medical care or start jobs.

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Of 33,252 applications to the Department of Health permit scheme from July 9 to September 14, when the probe was launched, only eight per cent were granted.

An investigation into the COVID-19 related state travel exemptions was launched back in September.

In all, the watchdog received 315 complaints including from jobless stranded residents paying double rent, caravanning pensioners without internet being asked for documents they did not have, and a farmer who feared having to put down her animals.

It found that 33,252 exemption applications were received between July 9 and September 14.

Only 2,736 applications were granted.

Ms Glass said people felt caught up in a "bureaucratic nightmare", resulting in outcomes that were "downright unjust, even inhumane".

"It appeared to us that the department put significant resources into keeping people out rather than helping them find safe ways to get home," she said.

Related: NSW-Victoria border closure affects Echuca residents, businesses

Ms Glass did not criticise the decision to close the border.

She said the decision referred to public health advice, considered the human rights implications, and allowed for the exercise of discretion.

However, while discretion to approve exemptions was available, Ms Glass said it was exercised narrowly, and most applications did not even reach a decision-maker.

"People's anguish when they spoke to us was palpable," she said.

"I recognise that the Department of Health's intentions were to protect people in Victoria from a dangerous virus that had already seeded through cross-border incursion, and that the department was under enormous pressure dealing with the exigencies of the public health emergency.

"While we did not review all decisions and I do not suggest that all were unfair, the overwhelming majority of applications did not get to a decision-maker at all, and the guidance did not change even as case numbers in Victoria grew and the risks evolved.

"The consequences of that were vast, and unfair, for many thousands of people stuck across the border."

The team responsible for border exemptions was scaled up from 20 staff in early July to 285 by early September.

Those responsible for categorising and prioritising applications were expected to complete 50 per hour - an average of almost one every 30 seconds.

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The state government has been urged to acknowledge the distress the system caused, improve policy and guidance for such schemes and consider ex-gratia payments.

The Ombudsman's Investigation into decisions made under the Victorian Border Crossing Permit Directions was tabled in Parliament on Tuesday.

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