But Deputy Prime Minister Michael McCormack argues the opposition's concerns about the project amount to "cheap fear mongering".

Labor's infrastructure spokesman Anthony Albanese says the opposition supports the inland rail line but wants to put the blowtorch on the route selection process and financing arrangements.

"This is appalling. The government has botched this from day one," he told 2GB on Tuesday.

"It is very clear the government has failed to consult properly. It's very clear that there are real issues with the route going through prime agricultural land, that the locals aren't being listened to."

Farmers across NSW and Queensland are among those who have raised concerns about the lack of transparency associated with picking the route.

The 1700km project includes upgrades to 1100km of existing track and is mooted to start operating in 2024/25.

Mr Albanese said the government's route stopped 38km short of Brisbane's port rather than extending through a major urban area at considerable extra expense in order to "bodgy up" the commercial viability of the project.

Inland rail is funded by an off-budget equity injection into the Australian Rail Track Corporation, a model which requires net economic benefit to Australia.

A Shorten Labor government's inquiry would be led by an "eminent Australian" who would get access to Infrastructure Australia and other departments, including Finance and Treasury.

Mr McCormack is deeply skeptical of Labor's motivations.

"Labor's cheap fear mongering on inland rail is nothing more than an attempt to spread uncertainty and doubt amongst our rural and regional communities," he said in a statement on Tuesday.

The Nationals leader says regional farmers are eager to take advantage of the cheaper transport costs that will come with the project - which could save them up to $92 per tonne - as quickly as possible.

"When farmers hear that the feedback is 'get on with it'."

Community feedback into the design of the inland rail is being sought at the moment, after which the federal government will submit its environmental impact statement to the state government for approval.

The Australian Logistics Council says Labor's proposed inquiry must not delay construction on the project.

"By 2030, we will need to move more than 32 million tonnes of freight along Australia's east coast," ALC CEO Kirk Coningham said in a statement.

"We must find ways to do that which are safe, and which don't add to road congestion and other existing bottlenecks in the freight network."

The ALC is also pushing for port connections at both ends of the route.

Australian Associated Press