Services on several routes will be less frequent between Tuesday and January 28, with the changes mainly affecting the central belt, with some services from Edinburgh and Glasgow also impacted.
ScotRail says the reduced timetable will provide customers with greater certainty.
Passengers have been asked to check the status of their journey before they head to the station.
Alex Hynes, managing director of ScotRail, told the BBC’s Good Morning Scotland radio programme on Tuesday that the reductions affected around 160 of the 2,000 services the company normally runs each day.
Mr Hynes said: “We’ve got hundreds of staff across the business absent due to Covid.
“Where that affects drivers and conductors, clearly that results in cancellations.
“So, we’ve decided to proactively introduce a new timetable from today to operate slightly fewer services.”
Mr Hynes said he did not believe there was a higher rate of virus transmission among rail staff than the general population.
He continued: “We’ve seen record case numbers yesterday, 20,000 in Scotland.
“The entire population is being affected by that – our crews are part of that population.”
Asked if the reductions may have to last longer than anticipated, he said: “One thing we’ve learned with Covid is it’s very difficult to forecast what will happen next and I suspect there will be a few twists and turns in the Covid story before it’s over.
“What we’re saying is that we’re going to operate the current timetable for the period of January, but clearly we keep this under literally daily review.”