Network Rail is being investigated over its poor performance on routes used by train operators Northern and TransPennine Express.
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.
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."