A decrease in travel and an increase in staff absence has affected several routes.Read more
Rail operator TransPennine Express (TPE) has been given until March to improve its performance by the team coordinating transport across the north.
It follows a period late last year when the operator returned the worst performance figures in the country.
Transport for the North, which advises the Government on northern England's transport needs, says TPE must now build back trust and deliver a service that's punctual and reliable.
The transport body added that the new £500m fleet of trains are welcome with the extra capacity "much needed" but service levels must be maintained as they're brought in.
Leo Goodwin, Managing Director for TransPennine Express said: “We absolutely agree that our customers should benefit from improved performance.
"We have been very open about the fact that this was nowhere near good enough before Christmas and we have apologised to our customers for this."
Rail passengers have scored train operator Northern as the worst provider in the country, according to a new report.
Just 72% of passengers said they were satisfied with the service they received in autumn 2019, according to watchdog Transport Focus.
Nationally, 82% of travellers were satisfied with their journeys - up three percentage points year-on-year.
Poor punctuality, timetable chaos and industrial action saw the satisfaction score sink to 79% in autumn 2018, which was the lowest level since 2008.
Northern was the worst performer at 72%, with TransPennine Express coming in at 79%.
Meanwhile, Grand Central scored 94%, with Hull Trains coming third with 94%.
Nearly 28,000 passengers were questioned for the latest National Rail Passenger Survey.
The RMT union reckons that the government's £500m fund to restore historic railway lines closed more than 50 years ago is "PR spin way out of control".
General secretary Mick Cash says: "This is a bare-faced attempt to distract attention from the daily chaos on Northern, South Western, Trans Pennine and Britain's other basket-case franchises.
"RMT welcomes any investment in our railways but £500m is a drop in the ocean compared to what's really required to connect our abandoned communities and reverse decades of cuts to infrastructure and maintenance.
"The first step is to end the chaos, profiteering and fragmentation of privatisation. Anything else is just window dressing and no one will be fooled."
The chief executive of Network Rail, Andrew Haines, has apologised on behalf of the rail industry for train services in the North over the past few years.
Mr Haines was speaking after the Office of Rail regulation announced an inquiry into whether the government-owned infrastructure company had played a part in delays and cancellations that have plagued services run by Northern and TransPennine Express over the past two years.
Network Rail, which owns and operates rail infrastructure in England, Wales and Scotland, said about a third of the delays attributed to it were caused by external factors such as vandalism, cable theft, trespass and weather.
But Mr Haines told passengers in areas such as Cumbria: "We have let you down."
He said a cross-industry task force "has been pulled together to tackle the problems head-on" although he said there was "no quick fix".
A consumer watchdog, Transport Focus, has welcomed news that the rail regulator is examining how far Network Rail was involved in disruption to train services in the North over the past two years.
Both Northern and TransPennine Express, both of which run services in Cumbria, have faced heavy criticism because of cancellations and a lack of punctuality, but they have in turn blamed Network Rail's performance.
Anthony Smith, from independent watchdog Transport Focus, said: "While both Northern and TransPennine have rightly been in the dock over their part in delivering unreliable services across large parts of the north of England, it is only right the spotlight is now shone on Network Rail."
Locally the Lakes Line Rail User group said: "At long last a body has challenged the poor performance of the custodian, maintenance regime and operator, namely Network Rail. This is long overdue."