Mr Katter has written to Premier Campbell Newman demanding his government remove existing legal protections for bats, claiming the animals were "causing grief" in communities throughout the state.
He wants the law to be changed to allow landholders to remove bats from their property.
The Katter's Australian Party leader first wrote to the Queensland Government in 2011 calling for the laws to be changed.
He accused the government, which came to power a year ago, of ignoring the issue and said he had sought legal advice.
"It is now more important than ever that we change the laws that place more importance on protecting bats' rights than human lives," the Member for Kennedy said.
"We are now in a position where we can pressure Queensland Government ministers for the removal of the legal protection of bat colonies.
"We have had discussions with lawyers and understand that there are legal implications if the government does not act immediately."
The previous Queensland Government banned the shooting of flying foxes in 2008.
In September last year the Newman government changed the Nature Conservation Act to allow fruit growers to cull limited numbers of bats, but only as a last resort.
Mr Katter warned health issues would become worse in areas where bat colonies were "inundating schools, parks, playgrounds and other public areas".
He said Queenslanders' lives were at risk because Mr Newman was afraid to stand up to environmentalists.
"These creatures that are spreading through largely populated areas are rife with disease including SARS, hendra, salmonella, avian flu, leptospirosis and lyssavirus," he said.
From 1994 to 2012 there were 77 sporadic confirmed cases of hendra virus infection in horses, the Federal Government's National Pests and Disease Outbreak website read.
Most of these cases were caused by a "spillover of infection" from flying foxes - the natural hosts of this virus - and all occurred in Queensland and north-east New South Wales.
In February a horse died in Queensland's Tabelands area after contracting the hendra virus.
It came a month after a stock horse died in Mackay.