Total journeys in the year ending next Friday are expected to be unchanged on 2015-16 following the closure of the Queen Street tunnel in Glasgow for five months last summer.
That follows continuous growth from 57 million in 2002-03 to 93m last year.
A series of 12 days of strikes by conductors is also understood to have had an impact.
ScotRail operator Abellio has failed to hit undisclosed passenger and profit growth targets - meaning staff will be denied bonuses under a new scheme it introduced when it took over the franchise in 2015.
Unions said workers at sister firm Great Anglia, which is also run by Abellio, had received up to £500 each.
ScotRail is understood to view the halting of passenger growth as a temporary setback.
It is confident the total will rise again once two new fleets of trains have been introduced this autumn and next year.
This will be accompanied by 200 more services running daily by 2019, in the biggest expansion for a generation.
However, neither ScotRail nor the Scottish Government’s Transport Scotland agency, which controls the franchise, would discuss whether the impact on passenger numbers of the Queen Street tunnel work, which closed the main part of Scotland’s third busiest station, had been greater than expected.
Kevin Lindsay, Scotland district secretary of the train drivers’ union Aslef, accused the firm of going further by making other cutbacks.
He said: “The refusal of ScotRail to acknowledge the hard work of their staff is disappointing but not surprising.
“We are hearing reports daily from our members of Abellio’s cost-cutting measures.
“Drivers are reporting a shortage of uniforms and safety shoes. They’ve cut fruit and cereal bars from depots, which are used to fight fatigue.
“Abellio seem hell bent on milking the ScotRail franchise for every penny they can get.”
A spokeswoman for the ScotRail Alliance with Network Rail said: “2016 was a challenging year which had an impact on our profits, all of which, it should be made clear, are reinvested in the railway.
“We’re currently focusing in the areas that will deliver the best results for our customers, including £475m [on new trains] in the biggest investment since the Victorian era, delivering more seats and faster journey times for passengers.”
A Transport Scotland spokeswoman said: “We are delivering the most ambitious programme of rail investment ever seen in Scotland.
“Our railways are also more popular than ever, with up by a third since 2007.
“The planned introduction of modern longer, greener trains are to offer passengers more opportunities to make their journeys by rail.
“There is no target in the franchise agreement for overall passenger numbers. It incentivises the franchisee to grow patronage.”