Train delays and cancellations in 2014-15 have forced the UK's rail regulator to fine Network Rail £2m.
The Office of Rail and Road (ORR) said Network Rail's performance on lines in Southern, Govia Thameslink and in Scotland was "below expectations and missed punctuality targets".
Network Rail has apologised to its customers for their "disruption and frustration" however said it had invested more than £11m to "improve performance for Southern and Thameslink passengers" since the beginning of the year.
Managing director of Network Operations at Network Rail said: "At London Bridge we are undertaking the biggest and most complex station and track redevelopment ever attempted on Britain's railways - while simultaneously continuing to keep services running."
The regulator said Network Rail failed to liaise properly with operators to understand the extent of the disruption and had also used flawed data to compile timetables.
It added that Network Rail had "significantly underestimated the impact of the Thameslink programme on performance, which was further exacerbated by a timetable that was not robust".
Chief executive at ORR, Richard Price, said: "The scale of the delays suffered by passengers was central to our decision to fine.
"The penalty sends a clear message to the Network Rail board: Network Rail must urgently rectify these errors and deliver the reliability of services that passengers have paid for."
A spokeswoman for the ORR stated that the fine will either be paid to the treasury, or instead, will be used to improve customer service beyond what is normally expected.
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