The Local Government Association of Queensland says it has consulted with all councils to gauge a proper understanding of the wide-reaching problem.
The rebuttal comes after Premier Campbell Newman threatened to put his own workforce in trouble-prone areas - such as Charters Towers and Cairns - to combat flying foxes.
LGAQ president Margaret de Wit said she did not agree the bat issue was councils' fault.
"It's just not an easy issue," she said.
Cr de Wit said local and state governments needed to find a way to relocate flying foxes where the bats did not have an impact on urban areas.
"We have to somehow deal with it so the amenity of people is not being destroyed," she said.
"On the other hand they are important part of our environment.
"Local government and state government need to work together on this problem but what the solution is, I don't know at the moment."
LGAQ has recruited a environmental consultant to look into possible solutions.
Councils are allowed to apply for permits to use non-lethal methods - such as noise and smoke - to move flying foxes.
Environment Minister Andrew Powell said there had been instances where communities were concerned about bat roosts and councils had "not been willing to approach the department or take action".
"What the Premier outlined (Tuesday) is a step further - if councils do not proactively represent the wishes of their local community, the government will consider putting people on the ground to carry out the work," he said.
"However, this as an absolute last resort, and we implore local governments to listen to their communities.
"The Premier is right. There needs to be balance between community safety and flying fox protection and we hope this will encourage councils to act on behalf of their local communities."
While the Queensland Government last year overturned a ban on farmers, who had sustained crop damage, killing flying foxes with a permit, there is no intention to do the same for councils.
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