Network Rail is under investigation for its poor service on routes operated by Northern and TransPennine Express.
The Office of Rail and Road (ORR) said it had put the government-owned company "on a warning" for routes in the North West and Central region of England.
Performance deteriorated in 2018 and “failed to substantially recover during 2019”, according to the regulator.
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".
Earlier this month, Transport secretary Grant Shapps said Northern rail's service was "unacceptable" and that it could be nationalised within months.
The introduction of new timetables in May 2018 saw up to 310 Northern trains a day cancelled, and punctuality and reliability problems continue to blight the network.
Network Rail's contribution to passenger train delay minutes across Britain was 58 per cent in 2019, down 1.1 per cent compared with the previous year.