Lockyer Valley Regional Council is calling on the state and federal governments to help it move the proposed Inland Rail route, saying it would affect the 'nation's salad bowl' for 100 years.
The mayor and deputy mayor said the Helidon to Calvert route offered "no benefits" to the community and would increase flood risks, reduce connectivity and create noise and health concerns.
"We understand this is vital transport infrastructure and we aren't saying 'not in my backyard', but we are saying it must be moved outside of our townships," Mayor Tanya Milligan said.
"Our region has been put through the ringer with overlapping natural disasters and soon we'll have infrastructure of national significance dividing our towns in two and creating further hurdles to overcome on our journey to flood resilience."
The H2C project is one of 13 sections of Inland Rail being rolled out by the federal government-owned Australian Rail Track Corporation.
It comprises 47km of freight rail line to accommodate double stack freight trains up to 1800m, connecting Helidon and Calvert via Placid Hills, Gatton, Laidley and Grandchester.
The proposed design includes three road bridges crossing rail in Helidon and Gatton and one grade separated pedestrian bridge crossing rail in Gatton.
The section uses the existing rail corridor and the Department of Transport and Main Roads' Gowrie to Grandchester 2003 protected corridor.
Deputy Mayor Jason Cook said moving the route outside of Gatton might cost a little more but it made sense.
"... When picturing two kilometre long, double-stacked freight trains roaring through the centre of a busy town more than 40 times per day, realigning the route just seems like a no brainer," Mr Cook said.
Ms Milligan said despite repeated requests, the ARTC had been "unable or unwilling" to provide council key information, including costs of the planned infrastructure and the alternate route, specifics of the assessment process to compare options, or revised traffic modelling and safety assessments.
ARTC public private partnership director Tony Lubofsky said its additional studies to assess the feasibility of the rail line bypassing Gatton found "significant environmental and design challenges".
"[It found] additional impacts on koala habitat and prime agricultural land, increased flood risk, affecting new landholders, and extensive additional costs to the project," Mr Lubofsky said.
"... ARTC has undertaken extensive modelling on flooding impacts and shows that the proposed alignment does not exacerbate flooding in Gatton."
Currently, ARTC is preparing additional information for the H2C environmental impact statement.
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