Rail Freight Advisory Council chairman Peter Tuohey has been joined by a leading north-western transport operator, Ken Wakefield, and Premier Daniel Andrews in defending changes to the project roll-out.

He dismissed State opposition claims, at the Victorian Farmers Federation Ballarat conference, the project was in trouble.

"I think its making a political statement," Mr Tuohey said.

Victorian Nationals leader Peter Walsh told the conference he had real concerns about where the project was going.

"Tragically, and literally no pun intended that project has actually run off the rails," Mr Walsh said.

The $440 million project aims to upgrade and standardise the rail lines, out of the north-west to Melbourne.

The complete rollout will see an upgrade of 1113 kilometres of rail lines, from Geelong to Mildura, Manangatang, Sea Lake and Murrayville.

Mr Walsh said the project had been put on hold.

"One of the visions for Mildura, and container freight out of the north-west, was to actually have a 24 hour turn around to the ports, which makes the most efficient use of those train sets," Mr Walsh said.

"It's very, very disappointing to see that is a lot further away than it should have been.

"It takes two hours to get through the interchange at Ararat, which I think is just appalling."

He was joined by Western Victorian Liberal MP Simon Ramsay, who described it as a debacle.

"It's a mess.." Mr Ramsay said.

"What should have been a very straightforward project - worked on by the VFF for many years by going through all the spur lines that were important to you - has descended into a debacle."

Garry Bibby, crop grower, Berriwillock, said he was on the Sea Lake line, which had rotten sleepers and poorly welded rails.

"That's going to push a lot of trucks onto the roads, its been an absolute debacle," Mr Bibby said.

"Its run $100m over budget and the Labor Party want to walk away from it.

"It's terrible, they have got to be held to account.

"They cant stop the project, it's got to go ahead."

But the claims were roundly rejected by Mr Tuohey.

He said industry was fully supportive of pushing the completion date out to 2020 for both the Ballarat Freight-Passenger Rail Separation Project and the remaining stages of the Murray Basin Rail Project.

Representatives of Wakefield Transport, Graincorp, Emerald, Cargill, Southern Shorthaul Rail, Pacific National and QUBE, who recently met in Melbourne, were happy with the extended timeline.

"The Ballarat rail separation project is around allowing freight to have its own access, and throughput through Ballarat, which is a huge improvement, because government has never put freight first before, "Mr Tuohey said.

"Having that Ballarat rail separation project is fundamental to speed times of rail to the port, by not having freight trains having to wait for passenger rail."

He said the Sea Lake and Manangatang lines would now be completed in 2020, after the rail separation project was completed.

The $130 million Freight-Passenger Rail Separation Project will deliver a number of track and signalling improvements, not included in the original Murray Basin project, as well as providing the infrastructure to support future increases in passenger rail.

The State government said it would ensure a minimum of 42 weekly return freight paths from the Murray

Mr Tuohey said it was important to recognise the Murray Basin project would be delivered, but the changes had been made to make sure there was as little impact as possible on grain freight transport to port.

The Sea Lake and Manangatang lines would be closed at a time when they would have the least impact on growers.

He said the time delay at Ararat was not of concern.

"I don't think there was one complaint, from the operators about Ararat junction," Mr Tuohey said.

Wakefield Transports Ken Wakefield said industry understood stage two of the Murray Basin rail project presented issues that needed to be fixed, before stage three could start.

"The need to get stage two complete and working as the scope of works outlined is the main game, so Maryborough to Ararat is the primary focus and the weak link at present," Mr Wakefield said.

The turn at Ararat to connect with the Australian Rail Track Corporation was critical to create the promised efficiencies.

"Delaying stage three is really the only sensible option, as this will give more time to ensure the timing and project delivery schedule is set in concrete and give surety to business," he said.

Mr Wakefield said changing the Manangatang and Sea lake lines to standard gauge would mean all freight trains would have to run through the incomplete Maryborough to Ararat line.

"This will only increase congestion on this section and exasperate the current limited pathing issues."

Mr Andrews said it was a complex project.

"The notion that this is a simple thing does, indeed, beg the question why wasn't it done years ago?," Mr Andrews said.

"I would challenge anyone who says its simple its not simple, its complex, its important and it needs to be done properly.

"Yes, it is frustrating, but sometimes complex projects take longer than people would like."