The Queensland Government is set to overhaul rules to allow some farmers to kill flying foxes, but it says permits will only be issued to farmers as a last resort.

The animals can spread the potentially deadly hendra virus and have caused major concern in Queensland towns including Charters Towers, Barcaldine, Gayndah and Bargara.

Environment Minister Andrew Powell says there will be a faster approval process for permits, so councils can act quickly should large colonies seek to return.

But he says there will be no large-scale culls.

"The approach that a number of horticulturalists in particular are looking at is limited permits," he said.

"By limited we're talking in the range of 50 flying foxes per season.

"Their belief is that if they're able to shoot the scouts early in the piece it prevents more flying foxes coming to their crops.

"As I said we're reviewing that option at the moment."

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He says the Queensland Government's management policy aims to balance community safety and wildlife protection.

"Farmers will need to demonstrate that they have tried more humane methods of relocating or moving on flying fox communities from their crops," he said.

"I don't see this as something that will be used significantly and I think that message needs to go out to the community.

"I think there is a bit of hysteria form some of the more extreme environmental groups that are suggesting that this is open season on flying foxes.

"This is about restoring balance."

'Humane way'

North Burnett Mayor Don Waugh has welcomed the changes, saying a colony of more than 300,000 bats has been living in Gayndah for more than three years.

He says current eradication methods are not working.

"The previous actions taken were strictly controlled by the Department of Environment and the measures that they could take were very limited," he said.

"It's not a case of mass shooting - if there's a more humane way people will be quite prepared to take it.

"At this stage there isn't anything that's been allowed under the present rules that people have been able to take."

Mr Waugh says the decision is long overdue.

"We've had them living in the trees in the school grounds, to the extent that the children at St Joseph's school couldn't even use their playground because of the bat problem," he said.

"That in the school, that in the business section, that in the residential section - it's been a total indictment of our situation that we couldn't do something about them more seriously."

The mayor-elect of Charters Towers, Frank Beveridge, says the kill permits would be a last resort for the town where a colony of bats has been roosting in a park for more than a decade.

"Nobody wants to kill all the bats in Charters Towers, but we have to remove them and improve the lifestyle and mental wellbeing of the people living around the park," he said.

"This all of a sudden opens up many, many options that we couldn't use before."

Mr Beveridge says Charters Towers residents have tried everything to get rid of the bat community.

"The average bat has a brain capacity of a four- to five-year-old child so they learn very, very quickly that if there's noise or non-harmful things, they quickly learn to ignore it," he said.

"That's the problem with every one of the removal solutions we've found."