Fewer than two-thirds of South-West Trains' key commuter services ran on time in 2013/14, Network Rail accounts reveal.
The "real-time" figures differ from those normally released, which say commuter trains are late only if they arrive more than five minutes after the scheduled time.
South-West Trains managed a real-time punctuality rate of 65.7 per cent.
Manuel Cortes, TSSA union general secretary, said: "Even given the bad winter weather, these figures show that the private rail firms are still not delivering the levels of service that passengers expect.
"These figures show the daily reality of persistently late and cancelled trains for millions of passengers who are facing yet another increase in fares."
A spokesman for the Rail Delivery Group, which represents Network Rail and rail operators, said: “More than nine out of 10 trains arrived as planned in 2012-13, which meant 600m more punctual passenger journeys compared to 1997-98."
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