ScotRail has been fined £380,000 for failing to meet several benchmarks on performance for both trains and stations.
The train operator fell short of the required standards standards for station litter and toilets, both in stations and on trains, as well as the quality of seating and passenger information on board.
But the annual evaluation of ScotRail's rail and passenger service showed improvements in other areas such as customer care. Toilet facilities have improved in the past year, even though they missed their target.
The company said its performance was steadily improving year on year, pointing out that the latest fine was 16.5% down on the previous year and 60% lower than in 2009.
Steve Montgomery, managing director of ScotRail, said: "We welcome this third consecutive fall in penalties, which underpins steady progress in performance and tackling the challenges set by one of the UK's toughest regimes. It is a tribute to staff efforts and initiatives put in place.
"There is still work to be done and our focus on standards and investment in stations and on trains to meet customers' needs and expectations will continue."
Transport Scotland's Service Quality Incentive Regime system (Squire) monitors services and facilities at stations and on trains across the country, looking at 36 different areas.
Of the 17 areas in which performance was detailed on the national agency's website, ScotRail exceeded 10 of the benchmarks set and failed to meet seven.
Squire targets say that 97% of station toilets and 90% of toilets on trains must be open, sanitary and fully functional. Figures for the last quarter of 2011-12 show ScotRail failed in these, achieving 94.6% for toilets at stations and 86.59% for those on trains.
Checks on trains also look at whether the seats are undamaged, clean and fit for purpose. ScotRail achieved 84.4% on this, against a benchmark of 90%.
Stations are also inspected for litter and sanitation. ScotRail managed a performance level of 90.11% against the benchmark of 95%.
For passenger information on trains, checks are made to see if the final destination is displayed on the front and back of the train, as well as on any internal destination boards. Information displayed inside the train must also be accurate and legible.
ScotRail achieved 87.59% for this, against a target of 95%.
Infrastructure and Capital Investment Secretary Alex Neil said Squire was"one of the toughest regimes in the UK, with targets set as high as 99% for aspects of rail travel which we know are important to passengers".
He said: "It is a credit to ScotRail that customer satisfaction remains higher than the UK average, but they know they must not rest on their laurels.
"We want to see the trend of the substantial shift from road to rail, which has resulted in more than 81 million passengers travelling on ScotRail services this year, continue. And better trains, stations and services will play a major part in that.
"Over the past 12 months ScotRail has improved performance in a number of key areas and Transport Scotland will continue to highlight areas where further improvements are required to ensure that standards are high for rail passengers in Scotland."
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