Robert Roulston has been replaced by prominent owner David Moodie as chairman of Racing Victoria after an irregularity regarding his nomination of a horse for last year's Melbourne Cup came to light.

In his role as a bloodstock agent, Roulston nominated an overseas horse for the Melbourne Cup but after the sale fell through and the horse did not come to Australia, he advised RV a fee did not apply.

Roulston eventually paid up on advice the fee could not be waived but an internal audit process uncovered his initial non-payment request.

At a Racing Victoria board meeting on Friday, Roulston accepted responsibility and resigned as chairman, a position he held for two years after joining the board in 2008.

"As chairman I understand the need to set the highest standards of governance and probity and as a result I believe my action is right and proper," Roulston said.

"I wish Racing Victoria all the best for the future and will now focus on my other business interests here and overseas."

Moodie is one of Victoria's biggest racehorse breeders and owners and has been a director of RV since 2009.