It came as the train operator told The Scotsman it was still relying on staff volunteering to work overtime to cover its reduced timetable, even though most drivers have stopped offering because of their union Aslef’s pay dispute with the company.
At least 24 trains were cancelled for all or part of their journey, delayed or operated with fewer than the normal number of carriages on Sunday, increasing the potential for overcrowding.
Trains cancelled included four services between Edinburgh and Dundee, one between Inverness and Glasgow and two between Aberdeen and Inverness.
Shorter distance trains cancelled included several between Edinburgh and both Fife and North Berwick.
The changes came on top of ScotRail cancelling 532 of its normal 1,088 Sunday services as part of a temporary timetable introduced last week “to provide greater certainty and reliability for customers”.
The Sunday before that, 320 trains were cancelled because of a shortage of drivers.
ScotRail said there were 18 services altered or cancelled on Sunday due to “train crew shortages”.
A spokesperson said: “These alterations have occurred due to the fact that we still require a certain level of staff volunteering to work a Sunday.
"The service reductions are not the same across all depots, so for depots where there are fewer reductions in service we are still reliant on a certain number of drivers not declining to work overtime to fulfil the timetable.”
According to the official Journeycheck passenger information website, at least six other trains between Edinburgh and Fife operated with one quarter fewer carriages than scheduled.
Passenger YorkiePaul tweeted that the cancellations had left a four-hour gap between trains from Dunfermline to Edinburgh.
ScotRail responded: “I'm afraid it's purely because we have no other option, I'm really sorry.”
Travellers also complained of overcrowding on the Edinburgh-Glasgow route on Sunday, when trains on the main line were halved to hourly as part of the temporary timetable.
Lachlan MacNeil tweeted: “Service from Glasgow to Edinburgh if you get on is standing only. Crammed in like sardines. Can’t be safe and why are you paying full price to be stood up squashed. Absolutely woeful at best!”
ScotRail tweeted in response: “Services are running frequently between Glasgow and Edinburgh and a service doesn't leave the station if it's not safe and they're closely monitored throughout their journey. We always use every carriage that we can.”
Alexander Welsh tweeted: “Physically couldn’t get on my train from Glasgow to Edinburgh because every last carriage was filled to the brim.
"All carriages, even first class, were overloaded with people. Pressed up against the doors, standing single file down all the isles as well.”
Aslef’s executive committee is due to decide on Wednesday whether to put ScotRail’s revised 5 per cent pay offer to members. which union negotiators have recommended for approval.
However, it may take until mid July for ScotRail to restore its normal timetable because this would take up to ten days after the dispute is resolved, with any Aslef ballot expected to take three weeks to complete.