ScotRail's latest annual fare adjustment of 3.9% will take the price of a peak-hour return ticket between Glasgow and Edinburgh from £21 to £21.80.
Some cross-border services have seen even bigger hikes, with a walk up, return ticket for Virgin Trains' Glasgow to London service going up by 4.2%, from £121.60 to £126.70.
Sustainable transport charity Sustrans said passengers were being forced off trains by the fare hikes, which were going up faster than wages.
But they were defended by rail minister Norman Baker, who said tickets were "not nearly as expensive as has been presented". The Liberal Democrat minister conceded the current system, which sees the cost of regulated fares, including season tickets, increasing by the Retail Price Index +1% was "not ideal".
But he added: "Once you take the basket of fares, include early advance and off-peaks, we are not nearly as expensive as is being presented. But the basic premise that we continue to veer on increase above inflation – no we don't want that."
In Scotland, the price of train tickets is rising marginally less than the UK average of 4.2% this year and the gap in fare increases is due to widen. ScotRail has promised to freeze off-peak fares next year and in 2015, provided inflation does not rise above 3.5%, and peg any increase in peak fares to the Retail Price Index, as opposed to the RPI+1% formula used in England and on cross-border routes.
Transport Minister Keith Brown has also pledged to limit off-peak fare increases to RPI-1% when the ScotRail franchise is renewed in 2015.
Passengers at Glasgow Central Station yesterday criticised the new fares amid ongoing cancellations and delays to services.
Nicole Glen, a 22-year-old Glasgow University student said: "It's ridiculous. Every single year the prices go up. The trains here are notorious for providing a poor service and being overpriced."
Some commuters say they will be forced to consider alternative means of travel. Andrew Sim, a 30-year-old manager from Coatbridge said: "I am not happy as I regularly commute to Edinburgh. I would rather take my car but there are not enough parking spaces and petrol prices are also incredibly high."
ScotRail said it had worked hard to keep the increase down to a level that continues to offer value for money. A spokesman added: "Our approach enables us to invest in improvements including more and faster services and better facilities at stations and on trains."
Malcolm Shepherd, chief executive of Sustrans, said: "Many people are facing a stark choice – fork out for expensive train travel, own a car and cut back on essentials, or stay put and miss out on jobs and opportunities."
The Association of Train Operating Companies said fare increases reflected Government policy since 2004, which has sought to increase the share passengers pay towards running the rail network.
Its chief executive Michael Roberts said: "It is the Government, not train companies, that decides how much season tickets should rise on average each year."
But Shadow Transport secretary Maria Eagle claimed the Government had "caved in" to train operators by allowing some fares to rise by more than 4.2%.
She said: "People are paying more for a worse service."