Some 27 trains a day missed intermediate station stops between August and February, figures provided to Mid-Scotland and Fife Green MSP Mark Ruskell showed.
That compares to around 15 trains a day between January and August last year, and 20 for the whole of 2017.
The practice is aimed at minimising knock-on delays to other trains but has infuriated passengers left stranded.
Transport minister Humza Yousaf has called for it to be minimised, especially at peak periods.
In an answer to a Parliamentary question from Mr Ruskell, Mr Yousaf said: "Between 20 August 2017 and 3 February 2018, there were 3,684 separate incidences of skip-stopping reported to Transport Scotland.
"This is 1.06 percent of the total numbers of services planned to be run over this period (348,132 in total)."
The minister had previously revealed that 0.6 per cent of services skipped stops between 8 January and 19 August last year, or 2,903 of 474,570 scheduled to run.
He also said the rate was 0.78 per cent for 2017.
ScotRail operates about 2,500 services a day.
Thurso was the worst hit station in the latest figures, where 2.5 per cent of trains failed to call - or one in 40.
Scottish Greens transport spokesman John Finnie said: “It might seem a small proportion, but behind these figures is massive inconvenience encountered by commuters the length and breadth of the country on a daily basis.
"Stop-skipping leaves people stranded, with serious consequences for their work, education, childcare or even medical appointments."
Scottish Conservative transport spokesman Jamie Greene: “I met with ScotRail managing director Alex Hynes today and raised this very issue with him directly.
"The figures show an unacceptable rise in the practice of missing stops.
"I understand the reasons behind doing it to keep the network flowing, but to customers it is effectively a cancelled train and a huge inconvenience to them.
“Whilst I was re-assured that reducing this practice is a top commitment of ScotRail, the proof will very much be in the pudding on whether they can reduce it."
Scottish Labour transport spokesperson Colin Smyth said: “These figures are just not good enough and another example of ScotRail doing what they like while Transport Minister Humza Yousaf sits on the sidelines watching as passengers lose out.
"It is bad enough that passengers are having to put up with fares rising above wages, overcrowded and cancelled trains but even when their train isn’t cancelled, they are waiting on the platform worrying about whether their train will even stop."
However, the ScotRail Alliance with track owner Network Rail said the situation had improved over the last month.
It said the proportion of trains skipping stops between 4 February to 3 March was 0.7 per cent.
The operator also said that in Fife, where there had been some of the most vocal passenger anger, skip-stopping had fallen by 63 per cent between November and February.
An alliance spokesperson said: “Our performance hasn’t been good enough in recent months, but these figures show that things are improving.
Fewer than 1 per cent of all scheduled services missed a station in recent weeks, and we’re working hard to reduce this even further.
“Skip-stopping is something that we only do when absolutely necessary, to prevent further disruption across the network.
"We are very clear that it should always be a last resort.”