Unions have complained that the indemnity provision allows ScotRail to draw millions of pounds from the public purse when its employees go on strike.
They were backed yesterday in a report by the Infrastructure and Capital Investment Committee (ICI) of the Scottish Parliament, which called on ministers to consider removing the clause when the ScotRail franchise is renewed in 2014.
However, the Conservatives' sole representative on the committee, Alex Johnstone, MSP, dissented from the finding and warned this would risk provoking more strikes, worsen disruption for passengers and add to the cost of running Scotland's railways.
"One of the reasons unions take strike action is to intimidate employers. This clause limits the ability of trade unions to do that by indemnifying the franchisee," Mr Johnstone said.
"Getting rid of this clause would strengthen the hand of the trade unions and undermine those who are doing their best to continue to provide services."
The existence of the indemnity clause was first revealed by The Herald's sister paper, the Sunday Herald, in January 2010 as ScotRail braced itself for a strike over whether train doors should be operated by drivers instead of conductors in order to cut staffing costs.
The controversial practice was eventually introduced and maintained on train services established following completion of the Airdrie-Bathgate railway, despite a series of strikes by the Rail Maritime and Transport (RMT) union.
In its report, the ICI committee pointed to claims by the RMT the indemnity clause did not provide an incentive to ScotRail to resolve disputes as it would "expect to receive compensation" from the Scottish Government".
"The committee suggests Transport Scotland explore whether it is possible to remove the indemnity clause from future rail franchise contracts in Scotland, and to examine the potential consequences of doing so," the report concluded.
A spokeswoman for Transport Scotland, the Government agency responsible for the ScotRail franchise, said: "We welcome the ICI report and the findings will be taken into consideration along with the consultation responses as we prepare the next franchise agreement."