Transport Infrastructure minister Jacinta Allan says upgrades to the project are ahead of schedule, with crews recently completing 109 kilometres of re-sleepering and ballast installation.

"These vital works will allow us to move more freight onto rail - boosting the safety, capacity and reliability of services and better connecting primary producers to our major ports," Ms Allan said.

"Our investment in Victoria's freight network will enable trains to travel faster, carry more and run more often - meaning we can move more product and create more jobs for Victorians."

But both the state opposition and lobby group the Rail Freight Alliance, which represents Victorian metropolitan and regional councils, cast doubt on the claims.

"The MBRP is stalled, astronomically over-budget and nearing a decade behind schedule thanks to Ms Allan and the government's project mismanagement," the opposition's spokesman for Regional Victoria Peter Walsh said.

"She has out-done herself with these false claims that will infuriate the regional Victorians who have missed out on Basin Rail's transformational benefits because of her mistakes," Mr Walsh said.

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Ms Allan said the MBRP works had seen more than 57,000 sleepers replaced and the installation of 30,000 tonnes of ballast.

The works were expected to be completed by mid-2022 and would remove most of the speed and heat restrictions that have limited use of the line.

The alliance delivering the works - which comprises ACCIONA, Coleman Rail and SMEC, supported by Rail Projects Victoria and V/Line - had been awarded the contract for the next package of works.

Further works include track upgrades on the Ararat to Maryborough Line and Merbein and Donald siding works.

Significant planning, design and industry consultation took place in 2021 in preparation for works on the Ararat to Maryborough Line.

Works were expected to be completed by the end of the year.

A modern signalling system would also be installed by V/Line at Ararat Junction to improve safety, efficiency and reduce transit time through the junction, with works now underway.

Design work and procurement was also underway on further upgrades, including new crossing loops and sidings, improvements to Maryborough and Dunolly junctions and signalling upgrades.

The government said the works would enable 49 train paths on the Murray Basin network, up from the current 28 paths, and it is estimated to remove around 20,000 truck trips off the road.

But RFA chief executive Reid Mather said despite the minister's comments, the rescoped project fell far short of the original promise and had not achieved the outcomes set out for it.

"A lot of it is rectifying works that went wrong, in the first place - they are putting back staging and passing loops, they removed some time ago," he said.

"The project is vital for Victoria's economic future by delivering Victorian produce to and from global markets, utilising rail to achieve this is critical," Mr Mather said.

"The completion of the MBRP will reduced truck movements, strengthen access to global markets, improve road safety and longevity, reduced congestion, improve amenity and decrease emissions."

He said the region was now worse off than before the works started, with both the Sea Lake and Manangatang lines isolated from the national rail network.

"The project has cost 50 per cent more to complete stage two of a five stage project, that was scheduled to be completed in 2018."

He said the failings of the project had resulted in additional truck movements putting pressure on the road network.

"I just want the minister to keep her original promise, do the five stages" Mr Mather said.

"Regardless of the spin, the outcomes haven't happened."

The minister's statement was reflective of progress on the revised plan - 'but that's not what our community, the RFA or the industry want - all they have left Victoria with is a gauge break."

"Mildura has access to the Port of Melbourne and the national rail network, if they go via Ararat."

The failure to complete the project to its original specifications highlighted issues with the national rail freight network.

"I think there are eight different signalling systems, across Australia, which makes it terribly difficult for national rail freight operators to manage.

"If you want to get into Melbourne you have to have agreements with the Australian Rail Track Corporation, Metro and V/Line.

"It's an overregulated and disconnected governance system, which has left us pretty poorly off."

Mr Walsh said under the project's original scope, first put forward by the coalition, north-west Victorians should have benefitted from a standardised freight rail network by 2105.

"Not only will Basin Rail, completed in full and to the original scope, deliver better productivity and efficiencies for producers and transporter in the north west, it'll also mean less damage to country roads by removing hundreds of truck movements every single day," Mr Walsh said.

"The commonwealth has gone above and beyond to get Basin Rail finished, providing a further $200 million more than 12 months ago to fix the Minister's botch job.

"But the future of the Project hanging in the balance because the Victorian government has refused to contribute a $5 million share for planning work to begin."