Borg claimed it was also underpaid more than $505,000 under a separate contract to clean train carriages at 22 stations and station facilities.
Borg’s staff also underwent Railway Industry Worker training in 2014 at V/Line’s request, but the documents allege V/Line refused to cover the cost of the training — $63,000.
V/Line admitted it withheld $153,720 from Borg between July 2015 and June 2018 under the washroom cleaning contract, but said this was because it received non-compliant invoices.
Its lawyers also claimed the agency received invoices for work performed by another company and for the cleaning of facilities that were not in operation.
V/Line claimed in its statement of defence that Borg failed to pay about $45,000 annually in rebate payments between 2012 and 2018.
The case comes as the Independent Broad-based Anti-corruption Commission is investigating V/Line, Metro Trains and the Department of Transport.
V/Line’s chief executive James Pinder has been suspended, along with Metro Trains manager Peter Bollas, while the investigation is under way.
After cleaning train carriages and stations for V/Line for more than a decade, Borg lost its contract to Transclean in early 2018. The contract has not been made public, but is understood to be below $10 million.
Transclean has been contracted to clean Metro’s trains since 2010.
It is not clear whether IBAC is investigating cleaning companies contracted by V/Line and Metro, and The Age is not suggesting this.
Borg’s general managing director Jeff Borg said he believed the court case launched in March last year was separate from the IBAC probe.
He says he has not been approached by IBAC investigators or involved in corrupt conduct.
Transclean’s general manager Nelson Aguila denied that his company was involved in corrupt conduct and said he would have an “open-door policy for any investigation at all”.
V/Line has been contacted for comment.
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Timna Jacks is Transport Reporter at The Age