Prime Minister Malcolm Turnbull has defended the federal government's decision to build the final leg of the Melbourne to Brisbane inland railway on a Queensland flood plain.
The government officially announced on Thursday that the route will run between Yelarbon and Gowrie, cutting directly across the Condamine flood plain in the state's Darling Downs region.
Farmers have hit out at the plan, with industry body AgForce saying it will have a "massive impact on local landholders and some of the best agricultural land in the country".
AgForce grains president Wayne Newton says it supports new infrastructure projects in regional areas, but not at the expense of places like the Condamine flood plain.
"Any impact on water moving naturally across the flood plain is a major concern as water is very hard to predict," Mr Newton said in a statement.
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He says landholders need several questions answered before work starts on the inland rail route, including how they will be compensated and move machinery if their land is dissected.
Mr Turnbull says there are plenty of railways around the world built on flood plains.
"There are a number of reasons for that alignment being chosen," he told ABC Radio.
"It uses existing rail corridors as much as possible and is a more economically viable option than the other routes."
But Southern Downs Regional Council mayor Tracy Dobie says she is disappointed the government has decided against building the last leg of the train line through her area.
"There is already a Queensland, state-owned rail link through the Southern Downs," she told ABC Radio.
Ms Dobie says it "didn't make sense" to construct another track and it could result in the state government abandoning the maintenance of the existing line.
"The impact on the economy would be devastating," she said.
Federal Transport Minister Darren Chester says rigorous technical analysis and consultation had helped the government decide on the preferred route.
Mr Chester reiterated Mr Turnbull's comments that it used existing networks as much as possible and also went past Wellcamp Airport, "which didn't exist in 2010 when the original route was considered".
"I acknowledge there will be impacts to those living and working on or near the preferred route," he said.
"The final design will be subject to an extensive state government planning and approvals process, which will work through questions about technical and environmental aspects."
