Housing Justice has deemed the discovery both surprising and concerning, given the protections in place for renters during the public health crisis.

The Council to Homeless Persons analysed Department of Health and Human Services rent reports dating from December 2019 - June 2020.

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Flora Hill - Bendigo East ranked third among the Victorian suburbs with the largest six-month rent increase, with a seven per cent rise.

The Melbourne suburb of Brighton East recorded the highest increase, at 11 per cent.

Meanwhile, rent in Moe - Newborough went up by nine per cent.

The Council to Homeless Persons said the analysis showed housing affordability was not just an issue in metropolitan Melbourne.

While Flora Hill-Bendigo East recorded one of the largest rent increases in the state, a number of other areas in Bendigo recorded rises of three per cent.

They included Bendigo itself, Golden Square - Kangaroo Flat, and North Bendigo.

Council to Homeless Persons chief executive Jenny Smith said the two regional Victorian suburbs with the largest rent increases had something in common - they were within about two hours of Melbourne.

She believed two things were happening: "People are saying, 'I want to get out of the rat race and move out of the city', and, 'I'm feeling financially insecure and I'm going to reduce my exposure through rental and move somewhere cheaper and commute or work from home'."

Ms Smith was concerned that meant more competition for affordable rental properties in those communities.

Haven; Home, Safe reported seeing huge competition for rental properties in Bendigo and renewed interest from people relocating from Melbourne.

Chief operations officer Trudi Ray was concerned the trends would drive property prices - and rents - up and create greater affordability issues for those who were struggling not just due to the pandemic, but because of other vulnerabilities.

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The Real Estate Institute of Victoria recorded a vacancy rate of 1.1 per cent for the Bendigo region, including Loddon, in August.

Elders Real Estate Bendigo only had only property listed as available to rent at the end of last week. Department manager Breanna Attard said there would normally be 10 or 15.

"People, during the pandemic, are staying where they are," Mrs Attard said.

But, in the event a property became vacant, owners had the opportunity to put prices up.

Mrs Attard knew of a property that became available for rent again at $20 more a week than it had prior.

The property, which was available for about the median rental price in Bendigo, was still getting "a really good response."

Mrs Attard said rental prices in Bendigo were steadily increasing - something reflected in the Council to Homeless Persons' assessment of rental data over 10 years.

"It's just with the real shortage, that's putting prices up. That's what we're seeing," Mrs Attard said.

She said the sales market was also strong, but many of those buying were owner-occupiers.

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Housing organisations and associations nationwide have been urging the federal government to invest in social housing.

Ms Smith - also the chair of Homelessness Australia - said the federal budget not only failed to invest in social housing growth, but would cut millions from homelessness services.

Housing Justice manager Kirsty Waller urged anyone whose rent had increased since the state government's moratorium came into effect on March 29 to seek legal advice.

The moratorium is set to continue until March 28, 2021.