The indemnity provision could cost millions to the public purse. ScotRail will hold negotiations this week with the National Union of Rail, Maritime and Transport Workers (RMT) over a dispute on who operates doors on a new Glasgow to Edinburgh train service, the Sunday Herald understands.

The existence of the clause sparked a furious reaction from the Tories and trade unions, which accused the previous Labour/LibDem coalition, which signed it off, of “subsidising” industrial disputes.

The RMT appears increasingly likely to ballot its Scottish members over proposals for train drivers, as opposed to conductors, to operate doors on a new Glasgow to Edinburgh service set to start later this year following a £300 million project to replace a rail link between Airdrie and Bathgate.

Under the terms of the 2004 franchise with ScotRail, Government ministers can cover the cost of a dispute if the company can show it has taken steps to avoid it and, if action goes ahead, can show that it has tried to mitigate its effects, which would result in conductors losing out in the event of a strike through loss of wages but ScotRail being covered by the public purse.

Transport Scotland, the Government agency responsible for the rail franchise, confirmed the clause could result in money being paid to ScotRail in the event of a strike but that this would be subject to ministerial approval.

A source close to the negotiations told the Sunday Herald that ScotRail was confident its costs would be covered. “There’s no way ScotRail would risk a strike if it wasn’t absolutely certain the Government was going to pick up the bill. It wouldn’t be in the company’s interest to lose millions for the sake of a franchise that is going to expire in a few years,” the source said.

Another source suggested the existence of the indemnity clause is thought to explain ScotRail’s decision to begin training managers and supervisors tomorrow to take over conductors’ roles in the event of a strike -- a move that has sparked fury among unions. Bob Crow, leader of the RMT, said ScotRail was being “deliberately provocative” and that it would struggle to convince ministers it had tried to avoid a dispute.

“Our argument is that ScotRail hasn’t taken reasonable steps to avoid a dispute. In fact it has been deliberately confrontational on this issue. If this did move to an industrial dispute there would be absolutely no ground for paying ScotRail out of the public purse,” he said. But he lashed out at the terms of the 2004 franchise, which was controversially extended in April 2008. “It’s a union-busting clause which I expect was demanded by private companies to take on the franchise. It’s exactly what’s wrong with the franchising system,” he said.

The original clause was agreed by then transport minister Nicol Stephen when Aberdeen-based First won the franchise to operate passenger train services in 2004. His predecessor and fellow Liberal Democrat MSP Tavish Scott is said to have confirmed to rail unions and the Scottish Trades Union Congress in March 2006 that ministers would approve a bail-out if the appropriate conditions have been met.

Stephen Boyd, assistant secretary of the STUC, criticised the franchise agreement, saying: “There’s no way a private operator who has taken on this franchise should have all its risk removed. If there is an industrial issue, the incentive is for the company to go into conflict, unlike normal industrial relations where the incentive is to avoid it.”

Alex Johnstone, the Scottish Conservative MSP and spokesman for transport, accused the LibDems of being wasteful with taxpayers money. “It seems to be typical of the attitude of Scottish Government ministers at the time who felt they could spend taxpayers money with absolutely indemnity,” he said.

The charge was rejected by the LibDems, whose spokesman said last night: “It is shocking hypocrisy from the Tories to criticise this sort of standard condition when they privatised the UK rail network in the first place. This is an entirely discretionary power.”

A spokesman for Transport Scotland said: “Other rail franchises in the UK have similar provisions.”

A ScotRail spokesman said: “We hope the meeting with the RMT will have a positive outcome. Meantime, contingency plans are underway to provide our customers with as robust a service as possible should the worst-case scenario materialise.”