The company recorded 97.3 million passenger journeys in Scotland in 2018, down from 98.4m in 2017.
However, the figures were still well above those recorded in 2016, when 91.8m journeys were made.
"In addition, there were engineering works across the country, including Aberdeen to Inverness, the Edinburgh to Glasgow line via Shotts, and the Stirling-Dunblane-Alloa route."
The company says that since the start of March it was operating more trains running on time than ever before - thanks to fleet expansion.
The Scotrail spokesman said: "That is a reflection we are now getting more of our new trains into service and completing major pieces of improvement works across the network."
After a weekend that saw what one railway worker described as the worst overcrowding at Waverley Station in 25 years, opposition politicians were unimpressed with the new figures.
Scottish Conservatives transport spokesman Jamie Greene said: "Given the dreadful performance of ScotRail and the sky-high fares, it's no surprise to see fewer people choosing to travel that way.
"At a time when we're supposed to be encouraging commuters to ditch their cars, train travel should be reliable, cost-effective and enjoyable.
"But it's none of those things, and all this makes a mockery of Nicola Sturgeon's supposed commitment to a climate emergency."
Labour and the Greens want to end the current ScotRail franchise of Abellio, which is a commercial wing of the Dutch nationalised railway.
They want to renationalise the train operator, to run on the country's publicly owned tracks.
Scottish Labour's Transport spokesman, Colin Smyth MSP, said: "At a time more and more people actually want to travel by train it says a lot about the poor performance of ScotRail that the rise in passengers has stalled.
"But given the catalogue of delays, cancellations, overcrowding and fare increases it's no wonder passenger numbers are on the way back down.
"Labour would put an end to this failing rail franchise and bring our trains under public ownership so have a railway that puts passengers first."
Scottish Greens transport spokesperson John Finnie said: "It's no wonder ScotRail has lost passengers.
"The company's service has been a shambles, relying on staff working long hours.
"Trains were cancelled at short notice, some didn't meet capacity and all the while fares have been increasing.
"People don't want to pay inflated prices for a poor service, but the reality is we need to shift people out of cars and into low carbon alternatives, such as trains.
"That's why we need to take ScotRail in the public sector, so it can serve Scotland's needs and tackle the climate emergency."
Mr Finnie's party tomorrow launches a Scottish New Green Deal, which is expected to promise new investment in growing and decarbonising Scotland's rail network.
A Scottish Government spokesman said: "Our investment in services and infrastructure is increasing capacity and services to the highest levels in a decade - 115,000 more seats, 2,400 services every weekday and more than 70 per cent of journeys are made on greener electric trains.
"We are working alongside ScotRail to build on these results to ensure they drive up customer service and satisfaction to where it belongs."