THE Melbourne to Brisbane inland rail line will not run past Warwick in a decision confirmed in Toowoomba yesterday.

The preferred route of the Yelarbon to Gowrie section will run from the New South Wales border through Millmerran, on to Brookstead and Pittsworth before connecting to the Wellcamp and Charlton industrial precincts in Toowoomba and heading east to Brisbane.

A route running via Karara and Leyburn, and the existing rail track past Massie were also considered.

Federal Infrastructure and Transport Minister Darren Chester said the decision had been a complex process and acknowledged there would be "some local impacts”.

"The selection of the preferred route for the Yelarbon to Gowrie section has been complex and I want to thank the community for its patience,” Mr Chester said.

"The government recognises the delay has caused concern, but it was important that we got it right.”

Member for Southern Downs Lawrence Springborg said while he had no preference, constituents deserved to see how the preferred route was selected.

"I want to be reassured that all aspects have been properly and transparently considered and not politically persuaded,” Mr Spingborg said.

"The inland rail must happen and there are few opponents to the project, but to accept the outcome people must be confident in the process.”