New electric trains are due to reduce trip times between Edinburgh and Glasgow from 52 minutes to 42 minutes in December 2018.
However, this is threatened because electrification work on other lines that feed into the route may not be finished in time.
The potential setback comes on top of separate delays to the £795 million Edinburgh Glasgow Improvement Programme [Egip] caused by faulty electrical components.
That is almost certain to postpone the start of electric services on the main Edinburgh-Glasgow line from July.
Hundreds of “Bonomi forks” installed along the line will have to be replaced.
However, electric trains cannot be speeded up until diesel trains, which have inferior acceleration, are also replaced on other routes which share the same tracks into the cities.
That will require electrification of lines from Dunblane and Alloa as part of a separate £93m project.
A letter from Network Rail chief executive Mark Carne to the Scottish Government’s Transport Scotland agency admitted there was not 90 per cent probability, or “P90”, that this would be achieved in time.
He wrote: “The current programme has a P90 date which is beyond Dec 18 and through continued discussions with the industry we are looking to improve that further.”
Mr Carne also said because of the problems with the main Edinburgh-Glasgow scheme, a different contractor - Carillion - might be drafted in for the Dunblane and Alloa work.
A rail engineering source said: “P90 is the earliest completion date for which there is a 90 per cent probability. As this is after December 2018, it puts the target of a speeded up Edinburgh-Glasgow timetable in December 2018 at risk.”
Another source said some 42-minute trains could run so long as electrification was completed as far north as Larbert by May 2018 so diesel trains from Dunblane could miss out intermediate stops.
A Transport Scotland spokeswoman said: “We have asked Network Rail to identify the best solution to their current electrification issues with clear focus on the needs of passengers and the priorities of Scottish ministers, including a fastest journey time of 42 minutes between Edinburgh and Glasgow city centres by December 2018.”
Network Rail said it had launched a review of Egip and would provide an update when it was completed.