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.

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.

Some were rendered effectively homeless and others distressed by the "traumatic" experience.

One family said they were treated "inhumanly" as they waited to be with their dying daughter, while another person missed their father's death after being knocked back.

When Fiona needed to travel to Victoria from Canberra to care for her 49-year-old intellectually disabled sister with terminal cancer, she was asked to provide a statutory declaration from her 86-year-old mother to explain why she could not do it herself.

Ms Glass did not criticise the border closure to COVID-stricken Sydney and parts of regional NSW in July, finding it was lawful and needed to protect people in the face of a public health emergency.

But she hit out at the narrow use of discretion and lack of reasons for refusals or avenue of appeal, adding the "overwhelming majority" of applications didn't even reach a decision-maker.

The risk-adverse system led to some of the "most questionable decisions" she has seen during her seven years in the job.

Despite scaling up its exemption team from 20 staff in July to 285 by early September, those responsible for categorising and prioritising applications were expected to complete 50 per hour - or one every 30 seconds.

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 wrote.

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.

"If there is a next time, we cannot let this happen again," Ms Glass said.

Opposition health spokeswoman Georgie Crozier wants Premier Daniel Andrews to go further and apologise for the now-abandoned permit and exemption system "aimed to keep people locked out no matter the circumstances".

While the government is still considering the ombudsman's recommendations, it maintains the "extreme risk" zone declaration was made to safeguard Victorians from the highly infectious Delta variant.

"The restrictions were necessary to protect all Victorians from risk - particularly as only 17 per cent of Victorians 16 years and older were fully vaccinated at the time," a government spokeswoman said.

Last year, the Victorian government refused to apologise after Ms Glass found it breached human rights by suddenly locking down 3000 Melbourne public housing tower residents without warning in July 2020.

The latest report comes as Victoria recorded 1185 new COVID-19 infections and another seven deaths on Tuesday.

The health department also confirmed genomic sequencing is underway on the state's first potential Omicron case after a fully-vaccinated international traveller returned a positive test on Monday.

Australian Associated Press