The head of V/Line says his organisation has been helping recipients of a scheme, which encourages freight transfer from road to rail to deal with its axing.
V/Line chief executive Matt Carrick noted the Victorian Auditor-General had reported three of the four services receiving Mode Shift Incentive Scheme funding "would not likely to be viable without it."
In the May State budget, the government extended the scheme for a final year, saying it would end on June 30, 2024.
Operators have expressed concern over the decision.
The Victorian Auditor-General Andrew Greaves has released his report on the Effectiveness of Rail Freight Support Programs, the MSIS and Port Rail Shuttle Network.
He found neither had 'fully realised the government's intention to move more freight by rail.
"Although the MSIS has kept some containers on trains that would have likely gone to trucks, it has not increased rail's share of container freight in regional areas," the report found.
"Delays in delivering the shuttle network facilities and services mean the social, economic and environmental benefits from diverting metropolitan containers from road to rail are also delayed."
Mr Carrick said "V/Line and Freight Victoria had been working with the three MSIS recipients (Seaway, Merbein, Westvic Container Export and Linx Portlink, Tocumwal) operating on the V/Line network to assist them to transition to successful operations, without the scheme.
Initiatives to assist operators included siding extensions at Merbein, to allow the stabling of 1200 metre trains.
There was a successful trial of the first of two 1500m trains, with the aim of extending the Seaway intermodal to 1500m.
"This train has been proposed as having a maximum trailing capacity of 4560 tonnes and if implemented would be the largest regional intermodal service in regular operation on the Victorian network," he said.
The Emu crossing loop had also been extended, to allow Seaway to operate twin 1200m trains, doubling services to six a week at 21-tonne axle load.
There had also been a 860m loop installed at Boorcan, to increase train lengths from Warrnambool from 320-880m.
A further crossing loop at Murchison East would allow the Linx train to increase in length from 900-1200m.
Department of Transport and Planning secretary Paul Younis told the Auditor-General his organisation was committed to continuing to work with industry to maximise the use of rail assets to encourage the shift of freight from road to rail.
"DTP welcomes the findings in the report that the Mode Shift Incentive Scheme kept container freight on rail that would likely otherwise have gone to road," Mr Younis said.
He said the department would continue to "effectively manage" the Port Rail Shuttle Network contracts and work with private sector proponents to minimise delays, achieve milestones and achieve private sector co-investment and construction.
"DTP acknowledges the report's findings of a range of external circumstances, beyond DTP's control, that have caused delays in the completion of the PRSN terminal works, such as COVID-19, impacts on business and more recent impacts associated with flooding of work sites and other environmental factors," he said.
He said the department accepted the need to examine the feasibility of the claim 30 per cent of metropolitan containers would be carried on rail by 2050.
"The statement was an expectation, based on earlier forecasts with lower growth than currently being experienced and required other supporting infrastructure," he said.
"DTP will reassess the proportion of metropolitan containers the PRSN is capable of taking at current and forecasted growth rates as part of network operational planning."