V/Line's acting chief executive Gary Liddell has rejected any conflict of interest in V/Line's decision on one of the bus companies it has selected to replace trains on the regional rail system.

A temporary five-week train and bus timetable has been introduced by V/Line while it tries to solve issues with the network caused by problems with carriage wheels and boom gates.

Bendigo Coachlines, a company which won one of the replacement contracts, is run by David Dawson, who is married to rail company chair Jenny Dawson.

Mr Liddell said the board was not involved in the decision and the contract was negotiated by a third-party provider, overseen by senior V/Line staff.

"We've employed a third party to actually make sure that we have the available replacement coaches for this service and they are going to be the most efficient and effective way of replacing those replacement coaches," he said.

"There is no direct involvement from either the board or from myself or anyone else senior at V/Line.

"I'm very confident that the appropriate steps have been put in place to make sure that's distanced from the day-to-day operation of what we do at V/Line.

"The board is always required to declare its interests and the absent themselves from any decision that might involve those interests."

In a statement, V/Line said Ms Dawson declared her husband's interest in Bendigo Coachlines before she was appointed to her role as chair of the board.

"Under the standing board protocols for the declared interest, Ms Dawson would not participate in any discussion or matters relating to Bendigo Coachlines," V/Line said.

"Yesterday more than 200 coaches provided V/Line services of which five were operated by Bendigo Coachlines."

Frustrated V/Line passengers have been warned the disruption to Victoria's regional rail services will drag on for months.

Rail services are not expected to return to normal until June and it has been estimated that free travel for commuters has cost V/Line $2 million a week.

Passengers who have been forced to catch buses instead of trains will still travel for free, but everyone else will have to pay the normal fare from Monday.

V/Line will be examined by a Victorian Parliamentary Committee next week.