There was major disruption across dozens of routes as seven times more alterations than normal were made to train schedules due to new services being launched.
Northern Rail said a shortage of train drivers was to blame for problems affecting destinations such as Manchester, Liverpool and Newcastle.
One in seven (14%) of its services were cancelled on Monday morning, with a further 17% delayed by at least five minutes.
Mayor of Greater Manchester Andy Burnham described the situation as "appalling" and claimed Transport Secretary Chris Grayling "needs to intervene today".
South-east England's Govia Thameslink Railway (GTR) - which consists of Southern, Thameslink, Great Northern and Gatwick Express - said services in its new timetable are being introduced "incrementally" as drivers and trains are redeployed.
A spokesman said: "Despite some cancellations, passengers will benefit from an overall increase in capacity with immediate effect."
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.
Angry passengers flooded train operator social media accounts with complaints.
One Twitter user posted a message to Northern Rail 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!!"
Another wrote to Thameslink: "Why have you introduced a new timetable with no new services to/from Hendon? Two trains cancelled at rush hour this morning. Shambles."
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?"
The firm told another customer that trains could be altered "for the next few weeks whilst getting everything into place".
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.
There will be almost 400 additional GTR trains every day.
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.
Robert Nisbet, regional director at the Rail Delivery Group, which represents the rail industry, said: "We'd like to thank customers for bearing with us as we introduce the biggest timetable change in a generation.
"In the long term these changes will see customers in many parts of the country benefit from more and faster services, better connecting communities and boosting the economy.
"Retiming over 100,000 services is a huge operational challenge.
"We're working together to deliver the best possible service but continue to advise customers to check their train times before they travel."
A demonstration will be held at London Bridge later in a row over help for disabled passengers using Govia Thameslink Railway (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.