A Senate inquiry has slammed Australia's biggest freight rail project.

The Inland Rail project is intended to build a 1,700-kilometre rail line connecting Brisbane to Melbourne.

The initial 2015 business case for Inland Rail said it would cost an estimated $4.7 billion. 

However, the Senate review found that the forecast cost has now ballooned to $14.3 billion and could exceed $20 billion. 

The 211-page report lays out dozens of recommendations to fix failures in consultation, technical modelling and route planning. 

Rural and Regional Affairs and Transport References Committee chair and WA Labor Senator Glenn Sterle says the project so far has been rushed and half-baked.

“The government will tell you about the good bits, but you can't keep covering up the ineptitude of the lack of consultation and poor route choice,” he said.

The scheme is being delivered through the government-owned Australian Rail Track Corporation (ARTC), but the report says an independent review is needed to update the original business case for accurate costing of the project.

The ARTC plans say that Acacia Ridge could be a termination point for the line, but that is still uncertain. The Senate report slammed the planners for their uncertainty, saying it was unacceptable given that a business case had already been lodged and parts of the line are already under construction.

It also calls for experts to look at extending the rail to Gladstone, 500 kilometres north of Brisbane, and building a passenger line from Brisbane to Toowoomba.

Community and stakeholder consultation by ARTC was deemed poor, leading Senators to recommend ARTC hold more regional forums to garner community support.

“When objectors want to have their voices heard they've been shut off,” Mr Sterle said.

Several local government areas in south-east Queensland do not want freight trains travelling through residential areas each day.

ARTC interim chief executive Rebecca Pickering said the authority knows there are matters of great interest for communities.

“We have heard the call from stakeholders who expected more from our early engagement on Inland Rail, and we have continued to improve as the project progressed,” she said in a statement.

On the finer points, the Senate report also said there are issues revealed by a draft independent study of the flood modelling used by ARTC for routes through Queensland.

“The concern about the ARTC’s flood and hydrology modelling has been validated and further fuelled by the independent panel's draft report that has identified a number of issues, many of which are highly significant,” the report stated.

The ARTC was called on to address the issues raised by Queensland's independent flood panel as a matter of priority.

Deputy Prime Minister Barnaby Joyce has issued a statement saying Inland Rail is vital infrastructure for regional Australia.

“The government will consider all recommendations in the Senate inquiry report into the management of inland rail and will respond in due course,” the statement said.

Mr Stearle said the Government would probably place the committee's report on “a dark shelf somewhere”.

“I have no doubt this government is going to try to bury it,” he said.