A £2 million fine levied on Network Rail for breaching its licence and problems such as massive disruption at a leading train station will lead to job losses and cuts to improvement works, it has been warned.
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.
But the decision to levy a fine was attacked by rail unions, who complained the tab will be picked up by taxpayers.
The money will go to the Treasury while previous fines have been spent on improving Wi-Fi services on trains.
Mick Whelan, general secretary of train drivers' union Aslef, said it was now time to renationalise the railways, adding: "Fining Network Rail is tantamount to picking the pocket of the taxpayer."
Southern and GTR represented a third of punctuality delays and almost half of cancelled and significantly delayed services in England and Wales, an investigation by ORR found.
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 and scenes of chaos 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.
"The scale of the delays suffered by passengers was central to our decision to fine."
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 £11 million 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.
"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."
David Sidebottom, of watchdog Transport Focus, said: "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."
TSSA union leader Manuel Cortes added: "This is worse than Alice in Wonderland. We take £2 million from one public body and give it to another public body, both of which are run by the Department for Transport.
"This keeps bureaucrats busy but it does not help one single passenger, upgrade lines or bring down the most expensive fares in Europe. It is simply a mad money-go-round."
A spokesman for Transport Scotland said: "We note the conclusions of the ORR's investigation on the reasons behind this and expect all recommendations to be reflected in full within the planning processes established under the new ScotRail Alliance."
Rail Minister Claire Perry said: "It is entirely right that the regulator should hold Network Rail to account for its poor performance and we expect the company to take decisive action to address the ORR's concerns."
Shadow rail minister Lilian Greenwood said: "Ministers have had the powers needed to get a grip for almost a year but they resisted calls to reform Network Rail and instead sat on their hands in embarrassment over their failing plans for the railways."