More than 2600 trains a year were classed as not having enough carriages or being too small to meet demand during rush-hours in 2010 and 2011, according to Government data.
In 2006, 1621 services were found to be "shortformed" – when the number of seats on key services do not match Scottish Government requirements.
Rail watchdog Passenger Focus expressed "disappointment" at the figures, which are being blamed on engineers failing to fix faulty trains promptly.
It called on the Scottish Government to ensure there are adequate facilities to maintain ScotRail's train fleet.
Robert Samson, the watchdog's manager for Scotland, said: "One of passengers' priorities is getting a seat and if a train is shortformed it leads to overcrowding."
Mr Samson said that shortforming problems had come about in part because of the increase in services introduced by ScotRail, which operates more than 95% of Scotland's passenger services.
The rise in shortforming in 2010 is thought to be due the winter and teething problems with electric trains on Inverclyde, Renfrewshire and Ayrshire routes.
However, the problems last year are thought to have been exacerbated by maintenance problems with ScotRail's 155 diesel trains. Most of their maintenance issues require a pit to access the underside of the train but only two depots, at Edinburgh Haymarket and Inverness, have such facilities.
A spokeswoman for Transport Scotland defended its record of investment, adding: "The context of the issue of short formations has to be seen in terms of the significant increase in services."
A ScotRail spokesman said: "Work continues with Transport Scotland and other stakeholders to support the increasing number of services we provide."
