Rail regulators have launched an investigation into Network Rail's performance after announcing the company was offering poor punctuality and reliability on some of the busiest commuter routes.
Network Rail (NR) reliability on routes such as Southern, Thameslink and Scotland was "below requirements", the Office of Road and Rail (ORR) said.
The overall trains-on-time figure was 89.6% - nearly 3% lower than NR's target of 92.5%, the ORR said.
Thameslink passengers have recently had to contend with upheaval caused by long-term work at London Bridge, while those travelling with Southern have experienced track and signalling problems.
Last Christmas there was travel chaos in north London after NR festive-period engineering work at King's Cross and Paddington stations overran.
Publishing a report on NR's performance for 2014/15 , the ORR said NR had not met a number of its enhancements programme delivery targets, with some projects facing delays.
The company has also delivered far less work than it planned for the upkeep of the rail network.
ORR chief executive Richard Price said: "NR has made a slow start in delivering on its enhancements and performance targets for CP5 (the period from 2014/15 to 2018/19) and we have asked it to demonstrate how it plans to get back on schedule to deliver on its commitments to 2019.
"The company is also falling short of its own targets on completing renewals works for the upkeep of the rail network. While there is good performance on the East Coast main line and the freight sector, overall reliability on some routes such as the Southern, Thameslink and Scotland routes are below requirements.
"We are investigating NR's performance improvement plans and delivery of enhancements. This work will help identify the issues the company needs to address to improve train performance, increase capacity and deliver on its commitments to passengers."
Responding to the ORR report, a Network Rail spokesman said: "We have recognised the scale of the challenge and have been openly reporting performance data regularly.
"There are clearly opportunities to improve following decades of under-investment in the rail network. However, it is worth highlighting that we operate the safest passenger network in Europe and the railway asset reliability is the best it has ever been.
"The increase in passengers means that more people are getting to their destination on time than ever before. NR's new leadership team, under chief executive Mark Carne, is committed to deliver the pace of change required to build a better, more modern network that passengers and businesses can rely on."
Transport Secretary Patrick McLoughlin said: "I expect the regulator to hold Network Rail to account. Performance must and should improve. The industry has to work together to address these failings and deliver for passengers and the economy, that needs to start now.
"More people than ever are travelling by train and through our long-term economic plan we are investing heavily in our railways to give passengers a better service and improve performance. NR and the industry need to ensure that passengers benefit as soon as possible."
David Sidebottom, passenger director at independent watchdog Transport Focus, said: "Passengers tell us that punctual trains are their main priority.
"Passengers welcomed news that there would be investment in schemes to deliver on their priority areas for improvement. It is disappointing that these are behind schedule. It is now vital that Network Rail is even more focused on delivering a good passenger experience through times of disruption due to these works."
Which? executive director Richard Lloyd said: "Long delays and consistently low levels of customer service are driving commuters to distraction, so we hope this investigation will get to the root of the problems.
"Passengers often have little or no choice as to the rail companies they travel with, so, as ticket prices continue to rocket, more must be done to improve customers' satisfaction and to get train timetables back on track."
The ORR said:
:: At the end of 2014/15 NR had missed 30 out of its 84 planned enhancement milestones with some projects facing delays or cost escalations;
:: NR track renewal is 7% behind plan, signalling renewals are 63% behind schedule, and overhead-line renewals are 77% behind target;
:: With NR failing to reach its punctuality figure, ORR has launched an investigation "to determine whether the company has done all it can to improve performance and punctuality on the network";
:: NR has implemented new plans and ORR's recommendations for engineering works to minimise impact on passengers following the Christmas overruns.