Up to four minutes could be added to around 100 of ScotRail’s busiest daily services from December.
Peak hour trains on lines into Edinburgh and Glasgow are expected to be the most affected.
The move comes as part of an extraordinary row over competing priorities between ScotRail and its track-owning Network Rail partners.
Network Rail sources said a “reality check” was needed because some trains regularly ran late due to increasing congestion as passenger numbers grew.
However, sources at train operator ScotRail said it would need more trains and drivers because of the widespread knock-on effect of slowing down the network.
ScotRail is appealing against the plans to the Office of Rail and Road, the rail regulator.
The firm is understood to be backed by ministers because they want faster rather than slower journeys as part of the ScotRail franchise to 2025.
A ScotRail source said: “Transport Scotland is fully supportive of our approach.
“If everything slows up and takes longer, at some point in the day you’d need extra trains and drivers to fill gaps.
“ScotRail has some of the best punctuality in Britain. The last thing we want to do is upset customers.”
Last month, 93.6 per cent of its trains arrived within five minutes of schedule - the standard industry measure.
The dispute is part of Britain-wide timetable review by Network Rail, against which some train operators south of the Border are also believed to have appealed.
In Scotland, it comes despite ScotRail and track owner Network Rail forming an alliance in 2015 to work closer together.
The dispute has arisen because the two bodies have been given different performance targets - set before the ScotRail Alliance was created.
This is despite the partnership being established to “enable both to work to common aims and objectives”.
While Network Rail is focused on improving reliability, ScotRail is seeking to reduce journey times.
In a letter to ministers this week, Network Rail chief executive Mark Carne said: “I believe strongly that we must improve timetable accuracy if we are to run the reliability of services that passengers increasingly expect.”
But he said its “key performance indicators” did not include journey time.
A spokeswoman for the Scottish Government’s Transport Scotland agency said: “We have asked Network Rail to work closely with the ScotRail Alliance to identify the best solution to timetabling, with a clear focus on the needs of passengers and the priorities of Scottish ministers in reducing, as opposed to extending, journey times wherever possible.
“Once again, this situation highlights the need for further devolution of Network Rail.”
The official passenger watchdog said travellers wanted both punctual trains and faster journeys.
Transport Focus senior stakeholder manager Robert Samson said: “Our passenger priority research identified that passengers’ want a punctual and reliable railway, with an improved frequency of service and reduced journey times, where possible.
“Any changes to timetables should be focus on those passenger priorities.”