Network Rail is being investigated over its poor performance on routes used by Northern and TransPennine Express.
The Office of Rail and Road (ORR) said it has put the government-owned company "on a warning" with regards to its performance in the northwest and central regions of England.
Performance got worse in 2018 and "failed to substantially recover during 2019", the regulator said.
Network Rail owns and manages most of the railway network in Great Britain, giving it responsibility for tracks, signals, tunnels, bridges, level crossings and most stations.
In 2019, Network Rail's contribution to passenger train delay minutes across Britain was 58%, down 1.1 percentage points compared with the previous year.
John Larkinson, chief executive of ORR, said: "The top priority for passengers is that their train arrives on time and that isn't happening consistently enough across the country.
"ORR is responsible for looking at how Network Rail contributes to train delays and while there are areas of very good performance such as in Wales and western region, Network Rail's performance in northwest and central region is not good enough.
"That is why we are putting the company on a warning to make sure its improvement plans deliver for passengers."
The ORR will look into Network Rail's recovery plan and analyse whether it is doing "all it reasonably can to improve service for passengers".
An investigation into TransPennine Express' poor performance found "it has been largely the result of train operations".
Network Rail chief executive Andrew Haines said: "For too many months, passengers - particularly in the Midlands and the North - have been coping with very poor train services.
"It simply isn't good enough and, on behalf of the rail industry, I'd like to apologise. We have let you down.
"There is no quick-fix, but fix it we will, and a cross-industry task force has been pulled together to tackle the problems head-on.
"I want them to cut through the red tape and deliver solutions quickly that will bring improvements for passengers in the near future.
"It will need more reliable assets, a much more reliable train plan and more robust operator resource plans."
He said Network Rail has made "good progress" in other parts of the country, with reliability at "record high levels" in some areas.
The investigation is just the latest episode in Britain's railway woes, with German company Arriva to be stripped of its Northern Rail franchise due to punctuality and reliability problems.
A government review into Northern Rail's finances, which started at the beginning of January, found it could only support operations for a "few more months".
For the majority of December, South Western Railway staff went on strike, affecting people going home for Christmas and travelling on New Year's Eve.
The company failed to reach an agreement with the Rail, Maritime and Transport union inthe long-running dispute over guards on trains.