Inland Rail is a 1700km line intended to link Melbourne and Brisbane via regional Victoria, NSW and Queensland.
When finished it is expected to reduce truck volumes across at least 20 regional towns, ease congestion on major highways, cut carbon emissions and provide a reliable network for producers, farmers and businesses.
A study released on Thursday has found the project, estimated to cost $9.3 billion five years ago, has blown out to $31.4 billion.
Report author Kerry Schott said the section between Melbourne and Parkes could be completed by 2027, but there was no indication of the timing of the project beyond this.
Dr Schott said while progress was being made in terms of NSW approval processes, Queensland's work was "well behind".
She would not "hang her hat" on the 2030s estimate for the Queensland leg of the project.
Transport Minister Catherine King said it would take a lot of work to get the project back on track.
"The previous government began this project with no idea where the rail line would start in Melbourne, and where it would finish in Brisbane, or how it would interact with towns, communities and the natural environmental along the route," she said.
Dr Schott found the government-owned Australian Rail Track Corporation did not have the expertise to manage the project, recommending Inland Rail be made a subsidiary company to allow it greater control of project management and approvals processes.
But the academic and Albanese government insist the project should go ahead.
"As it stands, Inland Rail is expected to accommodate and drive a modal shift of 200,000 trucks a year to rail, and this will bring significant benefits in terms of supply chain efficiencies, safety, environmental and congestion reductions," Dr Schott said.
Ms King said the government had accepted in principle or in full all of Dr Schott's recommendations, which would lead to "sweeping changes" to the project.
An independent cost estimator and value engineer will be appointed to undertake detailed assurance work.
Experts would also be added to the ARTC, with recruitment under way for an Inland Rail CEO.
"Inland Rail does remain an important project to meet Australia's growing freight task, improve road safety and to help decarbonise our economy, but we have been left with one almighty mess," the minister said.
Finance Minister Katy Gallagher, who is a shareholder minister in the project, said it would take 18 months to work through detailed costings.
About $2 billion has been spent so far.
Australia's largest state farming body said the benefits of progressing the project were clear and the government was right to progress it.
"A projected $10 per tonne saving for freight would help farmers make ends meet amid soaring food and fibre production costs," NSW Farmers Inland rail task force chair Peter Wilson said.
Opposition infrastructure spokeswoman Bridget McKenzie said the government should address the need for approvals by state Labor governments, which Dr Schott identified as a main reason for delays.
"The Albanese government should get on with delivering the Inland Rail, which is a nationally significant project," she told AAP.
