The Melbourne-to-Brisbane inland rail line will be built across the Condamine floodplain in Queensland, despite farmers' warnings that it could put lives at risk.

Federal Infrastructure Minister Darren Chester has written to residents informing them of his decision, which he is due to officially announce in Toowoomba later this morning.

An announcement had initially been expected earlier this year, but landholder concerns prompted a review of the four proposed routes.

Mr Chester said the relative cost and transit time were factors in making the decision, but he acknowledged "this decision will be disappointing for some" and "has not been taken lightly".

Loading...

The chosen route — shown in the map above as the purple line — is similar to the alignment known as the "base case" proposed by the Australian Rail and Track Corporation (ARTC) in 2010, but deviates east after the Condamine floodplain to go via Pittsworth, Brookstead and the Wellcamp-Charlton Industrial Precinct

Toowoomba's Wagner family built and owns the international Wellcamp Airport and had promised to invest millions of dollars in creating a road-rail-air transport hub geared towards food and agricultural produce if the rail corridor was shifted closer.

"While cost is not the overriding factor in decision-making for the preferred alignment, the Wellcamp-Charlton option has the lowest incremental cost compared with Base Case," Mr Chester said.

"It also offers the shortest transit time."

'It makes no sense to build across an extensive floodplain'

(L-R) Jason Mundt and Brett Kelly, with fellow farmer Wayne Saal. ( ABC News: Alexandra Blucher )

But floodplain grain-growers Brett Kelly and Jason Mundt have told the ABC the decision could be "catastrophic" for farmers.

They said flooding in 2010 inundated their farms, devastated crops, and dislodged a section of the existing railway.

As a result the line between Millmerran and Brookstead remains closed, the farmers added.

"It makes no sense to build the line across an extensive floodplain when there are better options upstream where there is less water," Mr Kelly said.

Mr Kelly and Mr Mundt said they had been told by ARTC the inland rail would be built on an embankment two metres higher than the existing line.

"If you consider building another line two metres higher, you're virtually building a dam wall, but without the same reinforcement," Mr Kelly said.

"It could definitely put lives at risk."

Landholders whose farms could be affected are furious. ( ABC News )

Mr Mundt said the higher embankment could see water back up for tens of kilometres in a big flood.

"You'll have people swimming out of their bedrooms, really," he said.

"If you thought Grantham was bad, you ain't seen nothing until something like that," he added, referring to the deadly 2011 flash flood in the Lockyer Valley town that killed 12 people.

Landholders at Millmerran, whose farms are now likely to be dissected, are also furious, saying the chosen rail corridor will cut through prime agricultural land.

"The final design will be subject to an extensive planning and approvals process, which will work through questions about technical and environmental aspects," Mr Chester said.

"I have asked the ARTC to work directly with affected landholders to refine the design of the railway."