The company has also given a termination notice to cleaning supplier Transclean Facilities.

V/Line said in a statement that the alleged conduct of Mr Pinder and Transclean was not acceptable to the company in any circumstances.

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Independent Broad-based Anti-corruption Commission began hearings on Monday, into allegations senior public officials improperly influenced the awarding of major contracts with V/Line and Metro Trains.

Mr Pinder was accused of using a secret burner phone, and having part of his Melbourne home paid off by a cleaning contractor.

V/Line chair Gabrielle Bell said V/Line would work to support front-line cleaning staff who might be affected by the decision.

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"All V/Line employees and contractors are expected to uphold the highest levels of integrity and the Board of Directors is committed to ensuring this happens at all times," she said.

Mr Pinder's termination takes effect on Thursday.

He had been suspended in August, ahead an investigation from the Independent Broad-based Anti-corruption Commission.