Lord Mayor Adrian Schrinner says the move is aimed at getting more properties onto the market amid a housing crisis that has left 50,000 people on the state government's waiting list.
He says the only incentive landlords need to relist their short-term rentals is the rate hike, as Brisbane's rental vacancy rate sits a 0.6 per cent.
"Renters are being affected with rents going up significantly, and then those that are wanting to get a rental property are having real difficulty at the moment to get access to anything," Schrinner told ABC radio on Wednesday.
"If owners had these properties in the market for short-term overnight stays, I mean, that is their choice, but what they'll be facing now is a 50 per cent increase in their rates.
"We don't want anyone to pay that, we want them to put those properties back into the rental market for longer term use."
Mr Schrinner said there were ample hotel rooms for visitors in the city, and council's priority is getting more Queenslanders into homes.
But short-term rental property owners aren't convinced the rate hike will work, warning it could have the opposite effect.
Shane Vollbon, who rents a property through AirBnB property, said demand was through the roof for short-term rental properties in Brisbane.
"I understand what the mayor's trying to do, but I think that that will cause a real problem in the short-term housing market that competes with hotels," he told AAP.
"We don't have enough hotels in the city, and if we did, we wouldn't be booked out 70 per cent of the time.
"I don't think that it's really going to change too much from a housing crisis issue, people are going to just pay more money for short term housing."
Queensland Council of Social Services said the state government needs to start building more homes to help alleviate rental property shortages, soaring house prices and the rising costs of living.
QCOSS and the Local Government Association of Queensland have been calling for a national housing summit for months.
"Queensland councils are united in the call for action to address the housing crisis and increased investment in social housing is critical," LGAQ chief executive Alison Smith said.
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