Network Rail is being investigated over its poor performance on routes used by train operators Northern and TransPennine Express (TPE).
The Office of Rail and Road (ORR) said it has put the Government-owned company “on a warning” in relation to its work in the North West and Central region of England.
Performance deteriorated in 2018 and “failed to substantially recover during 2019”, according to the regulator.
Industry figures show that in the 12 months to January 4, the proportion of scheduled train stops made within one minute of the timetable by Northern and TPE was 55% and 41% respectively.
This is compared with the average across Britain of 65%.
Transport Secretary Grant Shapps hauled the bosses of TPE, Network Rail and train manufacturers Hitachi Rail and CAF in for an urgent meeting last week to discuss their poor performance.
Earlier this month he said the Northern franchise will only be able to continue “for a number of months” according to the most recent financial information.
The department is considering whether to hand a short term management contract to the operator or to bring services into public ownership.
ORR chief executive John Larkinson 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 North West 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 investigate Network Rail’s recovery plan and analyse whether the organisation is doing “all it reasonably can to improve service for passengers”.
The regulator has also looked at the cause of recent poor performance by TransPennine Express and 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 added that Network Rail has made “good progress” in other parts of the country, with reliability at “record high levels” in some areas.
The organisation’s contribution to passenger train delay minutes across Britain was 58% in 2019, down 1.1 percentage points compared with the previous year.
Network Rail says around a third of the delays attributed to it are caused by external factors such as vandalism, cable theft, trespass and weather.