Federal Environment Minister Tony Burke has rejected calls to change the level of environmental protection for flying foxes so they can be moved.
Queensland Liberal Senator Ian Macdonald is pushing for a review to allow residents to move the animals away from homes.
He says the recent death of an eight-year-old Cairns boy from the bat-borne lyssavirus reinforces the need for action.
Yesterday afternoon, the Senate unanimously adopted a motion calling on the Federal Government to address the health risks posed by flying foxes.
However, Mr Burke says cooperation with the states is a better way to deal with the problem.
"I want it fixed and unless state governments are willing to sign a conservation agreement it won't be able to be fixed," he said.
"You don't need to dodgy up the science, you don't need to pretend a species isn't threatened when it is.
"All you need to do is allow the rules to be set down that allow flying foxes to be moved on quickly when they reach an urban environment."
Meanwhile, Bat Conservation and Rescue Queensland (BCRQ) says it is struggling to cope with a twofold increase in calls to remove bats.
BCRQ president Louise Saunders says her organisation has been inundated with calls since the Senate motion yesterday.
"We are run off our feet," she said.
"I don't know how we are going to cope and yet we are the stop-gap so that people don't get bitten or scratched.
"People are calling us constantly to rescue bats in situations where they aren't comfortable, in fact they are not supposed to be handling them or doing anything so they are calling us."
She says there is no need for scaremongering or culling.
"We totally agree that education is the key," she said.
"We need people to understand that they cannot touch any bat, flying foxes or micro bats.
"It's about being safe - if you don't touch and don't handle bats, you have nothing to fear."