The latest index into rental affordability shows the market is one the toughest ever for low-income earners in Brisbane.

Advocacy group National Shelter says pensioner couples are hardest hit, paying 59 per cent of their total income on rent.

The average household seeking to rent in Greater Brisbane are paying a quarter of their income on rent.

Spokesman Adrian Pisarski said the situation was similar in the Gold Coast region.

"As soon as you drop below average household weekly incomes of about $85,000 a year rents really start to look quite seriously bad across the board so when you are down at incomes around $50,000 for a household or less there is virtually nothing on the map that is affordable for rental," Mr Pisarski said.

The index compares rental data in the south-east region from 2000 to now.

"Over that period there may have been a couple of points that have been as bad as now but this is pretty much as bad as it has been even at the height of the mining boom," Mr Pisarski said.

"[The] level of affordability really isn't very healthy in Brisbane at all."

Nationally the index found part-time working parents and pensioners were priced out of the rental market in all metropolitan regions except in Perth.

"We have seen either a continuation of really poor rental affordability across the nation or a deterioration, with the exception of Perth," Mr Pisarski said.

"Perth has continued to slightly improve as the mining boom has come right off."

'Social exclusion and loneliness is a really big issue'

The Rental Affordability Index (RAI) is released on a biannual basis as an indicator on affordability relative to household incomes.

It is a joint initiative by National Shelter, Community Sector Banking and SGS Economics and Planning.

SGS partner Ellen Witte said when it came to inner-city housing for pensioners the situation was critical due to sky-high rents.

"It's increasingly difficult for these households to come by and with that, pensioners because of their older age would often have additional health costs and covering all that in addition to high rent would seem increasingly difficult," Ms Witte said.

For pensioners, living out of the city area poses challenges due to access to transport and healthcare services.

Ms Witte said it could also affect their mental health and wellbeing.

"Social exclusion and loneliness is a really big issue," she said.

"If you start to force people out of the communities they've lived perhaps all their lives and where their families and friends are, if they're being forced out because they can't pay the rent anymore it will obviously increase the levels of loneliness and things like that.

"Rents are most affordable in places where the least opportunities are in terms of jobs, services and education."

Ms Witte said older working women who were reaching retirement and have not been able to build up superannuation also have nowhere to go.

Affordability has also declined in regional Queensland with average rental households paying 24 per cent of their total income on rent.