Network Rail is being investigated for its poor performance on routes used by the train operators Northern and TransPennine Express, after problems with the track and infrastructure contributed to rail passenger misery in northern England.

The rail regulator, the Office of Rail and Road (ORR) said it had put the state-owned company “on a warning” in relation to its work in the north-west and central region.

The ORR said performance deteriorated in 2018, when delayed engineering works contributed substantially to the timetable chaos that led to thousands of Northern services cancelled or running significantly late. Although the industry vowed to learn the lessons, the regulator said performance had failed to substantially recover during 2019.

The mayor of Greater Manchester, Andy Burnham, has led calls from political leaders in the north of England for Arriva-owned Northern to be stripped of its franchise after years of poor service, although Northern has argued that most factors were out of its control – a position strengthened by the ORR’s conclusions.

Network Rail problems also contributed to the dismal performance of West Midlands Trains. Andy Street, the West Midlands mayor, has issued an ultimatum demanding improvement by the end of January, or he will call on the government to end the Abellio-owned franchise.

However, the regulator said that on neighbouring TransPennine Express, which introduced an emergency timetable in December to try to reduce its operating chaos and the number of last-minute cancellations, it had examined the causes of recent poor performance and found “it has been largely the result of train operations”.

The 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 is to investigate Network Rail’s recovery plan and analyse whether the organisation is doing “all it reasonably can to improve service for passengers”.

Overall, the regulator found that Network Rail’s contribution to passenger train delay minutes across Britain was 58% in 2019, down 1.1 percentage points compared with the previous year.

The ORR warned that “the current position is more serious than conveyed” than in assessments published by Network Rail itself. In a letter to the chief executive, Andrew Haines, the ORR said the company was “delivering close to the worst level of performance for five years, remains a long way adrift of its target and is tracking very close to the regulatory floor … This is not good enough for passengers.”

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.

He added: “There is no quick fix, but fix it we will, and a cross-industry taskforce 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.”

He said they had seen good progress in other parts of the country, with infrastructure performing reliably but admitted: “Recovering from any small incident or issue, be that a fallen tree, a broken-down train or track fault, on a congested and clogged network, remains our biggest challenge.”