Network Rail is facing a £2 million fine for a breach of its licence after an investigation by the rail regulator.
The Office of Rail and Road (ORR) said the firm's performance in respect of passenger services on Southern, Govia Thameslink Railway (GTR) and Scotland were "below expectations" and missed punctuality targets in the past year.
Southern and GTR represented a third of punctuality delays and almost half of cancelled and significantly delayed services in England and Wales, it was found.
ORR is proposing a £2 million fine, adding that NR has a chance to offer "reparations" to affected passengers instead of paying the financial penalty.
ORR said it found no systematic weakness in NR's performance delivery but it added there had been "repeated past errors" on timetabling, lack of liaison with operators and not planning ahead for passengers.
For Southern and GTR, there were "serious weaknesses" in data for new timetables.
The impact of work on Thameslink was "significantly under-estimated", which led to severe disruption at London Bridge station earlier this year.
There were "numerous errors" in Scotland in the December 2014 timetable caused by issues including a lack of quality assurance and detailed planning.
ORR chief executive Richard Price said: "Our investigation has identified important issues that Network Rail, working with operators, needs to address to improve performance for passengers on these routes.
"Our analysis shows that the company needs to develop a much better understanding of the impact of timetabling on the reliability of services and on rail users.
"These serious issues have caused severe disruption and frustration for passengers, most notably affecting services at and around London Bridge. ORR is therefore imposing a £2 million fine on Network Rail - a decision we did not take lightly.
"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."
Phil Hufton, managing director, network operations, Network Rail, said: "At the start of this year we had a number of problems that caused passengers disruption and frustration and we apologise for this.
"Since then we have proactively invested over £11m to improve performance for Southern and Thameslink passengers. This investment, which has seen the introduction of a revised timetable, improved equipment, the deployment of rapid-response maintenance teams at London Bridge as well as new information screens and better passenger information, is paying dividends and passenger service reliability has now improved by over 12% since January.
"While the nuts and bolts of our infrastructure are the most reliable they've even been, severe congestion caused by record numbers of trains and passengers makes delivering a consistently reliable service a daily challenge for ourselves and the train operators.
"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."
"As we are now a public sector organisation, the fine must come from within our existing budget, and will mean a reallocation of existing resources to pay it."
Mick Cash, general secretary of the Rail, Maritime and Transport union said: "With Network Rail a publicly owned body, the ORR imposing multi-million pound fines is effectively the taxpayer fining themselves and that is a ludicrous way to run a railway.
"The fines will have to be paid for by axing works or cutting staff , creating a vicious cycle of decline that is self-defeating and will just mean more fines and more cuts in the future which is a nonsense.
"There are deep-seated issues around fragmentation and a proliferation of contractors and agencies on our tracks , alongside a national skills shortage and budget pressures, which are compromising infrastructure projects and which will not be dealt with by handing out fines that simply compound the problems.
"RMT is demanding a coherent and joined-up approach to running our railways which of course means public ownership and an end to fragmentation and profiteering.
"If the money that is being bled out of our railways by the private train companies was reinvested in upgrading and improving services we would be able to meet all of the demands that are being thrown at us and cut passenger fares at the same time."
David Sidebottom, passenger director at the independent watchdog Transport Focus, said: "Passengers up and down the country, especially those in the south east, have been experiencing a poor service on their trains. Passengers expect to have a railway they can depend on.
"We welcome the regulator taking action. What is essential is that the penalty is invested by Network Rail in making an immediate difference for passengers."