Hundreds of trains were cancelled or delayed on Monday after a new timetable was introduced.
There was major disruption across dozens of routes as seven times more alterations than normal were made to schedules due to new services being launched.
Northern said a shortage of train drivers was to blame for problems affecting destinations such as Manchester, Liverpool and Newcastle.
By 4.30pm, 222 of its Monday services had been cancelled, representing 13% of its schedule, according to the trains.im open source website. A further 323 (20%) were delayed.
â ï¸ SERVICE UPDATE â ï¸— Northern (@northernassist) May 21, 2018
🔴Please see below for disruption on our network👇
📱For information on delays and cancellations, check before you travel: 👉https://t.co/6U2PzA1znQ
💷You can claim compensation here: 👉https://t.co/J1CCsJ3qI3 pic.twitter.com/UFLs7ZSQ8Z
Mayor of Greater Manchester Andy Burnham described the situation as “appalling” and said Transport Secretary Chris Grayling “needs to intervene today”.
The Department for Transport told the Press Association that neither Mr Grayling nor rail minister Jo Johnson were available to speak to the media.
A spokesman for Northern admitted it had been a “difficult morning” for some passengers, particularly on routes around north Manchester extending to Blackpool.
“We are very sorry for the delays and cancellations they have experienced,” he said.
Around 90% of Northern’s timetable has changed and an extra 1,300 trains per week are being introduced.
The spokesman added that this “remains a significant operational challenge”, warning that “localised service disruption” is expected to continue.
Govia Thameslink Railway (GTR) – which consists of Southern, Thameslink, Great Northern and Gatwick Express – saw 160 cancellations (7% of the schedule) and 213 delays (12%) by 4.30pm.
The operator said services in its new timetable are being introduced “incrementally” as drivers and trains are redeployed.
A spokesman said: “Today was a major challenge as the new timetable was tested on the first full working day. There has been some disruption in the morning peak and we apologise to passengers for any difficulties with their journey.”
He insisted that “overall the network coped well under exceptionally difficult circumstances” as the times of thousands of services were changed.
“We expect some ongoing issues and in the meantime we have already introduced more than 350 extra timetabled services this week,” he added.
â°🚉 Times are changing.— Southern (@SouthernRailUK) May 9, 2018
From Sunday May 20th, our new timetable will be in place. There will be changes to every train time and new journey possibilities.
Check your journey at https://t.co/Y0q94zRkRi
More info 👇 https://t.co/hU90huV4Op
The Aslef union said not enough drivers have been trained on new routes and rolling stock.
An official said the union had asked the company to start training drivers last summer, but it only started in February.
“Drivers are not on a go-slow, they are not calling in sick, but they just have not been trained on the new routes,” the official told the Press Association.
Anthony Smith, chief executive of passenger watchdog Transport Focus, said some Northern passengers “had a torrid time” and pledged to keep a “close eye on crowded services” run by GTR.
He went on: “Passengers will be pleased to see plenty of staff on the ground, but this is no substitute for sticking to the basic promise of the railways: running the trains on time.”
Angry passengers flooded train operator social media accounts with complaints.
One Twitter user posted a message to Northern which read: “Total shambles – first day of new timetables and it’s even worse than before – if that’s even possible! Your service is shameful!!”
A Great Northern passenger tweeted: “I organised my life around your new timetable – job, childcare, parking – to find the 8.57am train from Biggleswade into London doesn’t exist.
“I am now waiting one hour for another to get into work. Can you explain to my employer for me? Can you rearrange my childcare too?”
Drivers are not on a go-slow, they are not calling in sick, but they just have not been trained on the new routesAslef official
The timetable shake-up is designed to increase overall frequencies and reliability.
Many of the changes are a result of the £7 billion invested in the Thameslink programme in the South East, including rebuilding London Bridge station, new trains and track improvements.
GTR’s new timetable was developed from scratch and was designed to tackle existing issues by extending stop times at busier stations and increasing turnaround times at destination stations.
Some passengers in a number of locations have complained that they are being served with fewer or slower services, including in Hertfordshire, Bedfordshire, Kent, East Sussex and Surrey, where many people pay several thousand pounds for annual season tickets to London.
A demonstration will be held at London Bridge later in a row over help for disabled passengers using GTR services.
The Rail, Maritime and Transport union said the latest instruction from GTR tells staff not to attempt to place people of reduced mobility on a train if there is a possibility of delaying the service.
GTR insists it places a priority on making its services accessible to everyone and actively encourages people with restricted mobility to use its trains.
Disability campaigners and commuters will join the protest.