The rail contract extension was announced last year
The spending watchdog is considering whether to probe First ScotRail, after it overestimated passenger numbers.
Concern was raised after a report by Strathclyde Partnership for Transport, said 2008-09 passenger figures in the area were overestimated by 7.2 million.
Holyrood's audit committee has called in Auditor General Robert Black.
First ScotRail said it was correcting a "long-standing" error. Transport Scotland said it did not affect the extension of the rail franchise.
Passenger numbers for ScotRail as a whole stood at 81.3 million in 2007-08 and 84 million the following year.
Under the new calculations, the figures would be 74.5 million and 76.4 million over the same period.
Labour MSP Hugh Henry, convener of the audit committee, wants to know whether similar errors were made in previous years - and whether any mistakes could have made a difference to the Scottish Government's controversial decision in April 2008 to extend the First ScotRail franchise to run passenger rail services.
The cross-party committee, which recently held an inquiry into the extension of First Group's £2.5bn deal to run train services, raised concern over the level of information it was given during the probe.
Mr Henry said: "The committee was given incorrect information during the course of its inquiry which had to be corrected, and we expressed our concerns at the time.
"Now it transpires that inaccurate figures have been used as the basis for calculating projected passenger numbers in the SPT area, and this raises a question about whether this is the case across Scotland.
"Given we were told the success of the operation was a key justification for renewing the contract an error of this magnitude, with passenger numbers significantly overstated, gives me cause for concern."
The extension of the rail contract - the largest of its kind awarded by Scottish ministers - to 2014 was announced without widespread consultation.
The move led to concern among opposition parties, who questioned how transparent the process was.
A ScotRail spokesman said: "We are correcting a long-standing system error which pre-dates the current franchise. It had no impact on actual journeys made or on revenue.
"In fact, passenger journeys have grown 25% since the start of franchise."
The spokesman added: "The recalculation takes effect over the year ended March 31, 2010. It will better estimate rail journeys from Zonecards, a ticket which covers buses, ferries and the Subway as well as trains."
A spokeswoman for national transport agency Transport Scotland said the Zonecard calculation predated both Transport Scotland and the current administration.
She said: "The rate of passenger growth is accurately reflected in the figures with passenger journeys across the entire network increasing by 23% since the start of the franchise and this was a contributing factor in the decision to extend the franchise.
"The decision to extend the franchise is unaffected."