The same specialists told the hearing that education and risk mitigation were far superior methods of dealing with the endangered animals than killing or dispersing them.
Biosecurity Queensland scientist Dr Field Hume told the committee the hendra virus vaccine for horses would not only stop the animals being infected, usually through bat urine in their pastoral feed, but from passing on the virus to humans.
The hendra virus - usually transmitted through flying foxes - has caused more than 70 horse fatalities and four human deaths since 1994.
But Mr Hume said the single most effective method of reducing risk of the disease infecting humans was excluding horses from underneath trees where flying foxes were feeding.
He said 2011 brought more horse infections than ever before but there were no human cases which suggested risk management processes were working.
The committee is hearing information on land protection legislation amendments which will enable landowners to cull bat colonies and introduce penalties for disturbing their roosts.
Environment Department wildlife operations manager Mike Devery said two damage mitigation permits - enabling the scouts in bat colonies to be shot under a Newman Government plan announced in April - had been approved and one had been refused but he expected to receive many more.
He said those received were mostly from Bundaberg, Childers and Darling Downs areas.
Maryborough MP Anne Maddern, once a property valuer, asked whether the permits were limited to farmers or fruit growers who suffered economic loss.
She said she once had to assess an "unsaleable" property at Hervey Bay where the smell was so "atrocious" it made her eyes water.
Ms Maddern said the owners were suffering psychological issues because the smell and noise was so bad and people had stopped visiting them.
Mr Devery said permits to remove flying fox roosts considered human health and well-being.
But he said the bar had to be set high because there were 200 roosts in southern Queensland and dispersal could exacerbate problems in other nearby residential areas.
Mr Devery said it was better to mitigate the impacts through strategic clipping or clearing to create a buffer than to disperse them through loud noise, bright lights or pyrotechnics.
He said a health specialist would have to provide a direct link between psychological issues and flying foxes for a permission to rid bats for "well-being" reasons related to noise and smell.
Dr Frank Beard, from Queensland Health, said people's anxiety surrounding flying foxes was disproportionate to the low public health risk, usually due to inaccurate media reports.
He said educating people and mitigating the known low risks was a better plan than moving them on and "having unknown and unpredictable effect" which could lead to increased public health risks somewhere else.