A rail firm cancelled dozens of trains - hours after its new timetable began.
Govia Thameslink Railway (GTR) rescheduled every service on its Great Northern, Thameslink and Southern franchise as part of an overhaul billed as the biggest in the UK.
It said introducing the new timetable was a "significant logistical challenge" and apologised for "any inconvenience caused" to passengers.
It was unable to confirm how many trains had been cancelled on Sunday.
A GTR spokesman added: "We are introducing the biggest change to rail timetables in a generation and, as we have been informing passengers, we expect some disruption to services in the initial stages.
"This is a significant logistical challenge as we make rolling incremental changes across more than 3,000 daily services."
He added the timetable changes would mean a 13% increase in services across the GTR network.
The RMT and Aslef unions said they understood the disruption was because there were not enough fully-trained drivers.
An RMT spokesman said: "The union is still talking to members about the impact on the new timetable and plans to release further information on Monday."
The Thameslink, Southern and Great Northern rail franchise includes services to Bedford, Luton, Peterborough, King's Lynn, Cambridge, London King's Cross, London Moorgate, Wimbledon and Brighton.
No entire routes were cancelled on Sunday but "occasional trains" were not running, said a spokesman.
Frustrated passengers tweeted to complain about disruption on Great Northern services, with one asking "Any clue as to the reason? No drivers by any chance? Or explain the operational incident please."
The company replied: "Unfortunately we are not privy to this information".
Another stranded passenger wrote: "You've cancelled 5 (FIVE!!!) trains in a ROW between London and Stevenage, what an absolute joke" while another asked: "Surely you have had more than a year to plan your new timetable?"
⚠️A short-term amended timetable is in place across the Great Northern network.— Great Northern (@GNRailUK) May 20, 2018
🎫 - Ticket acceptance on: @CrossCountryUK@EMTrains@greateranglia@LDNOverground
ℹ️ Service updates and live departures - https://t.co/dGPkM54J9D pic.twitter.com/d1YcywG8u7
From Sunday, every schedule for Thameslink, Southern, Gatwick Express and Great Northern trains has been changed, in an attempt to improve rail efficiency in the South East.
It will mean 400 extra trains a day and new direct services from 80 stations into central London.
But passengers in a number of smaller locations complain they will be served with fewer or slower services.
'Doesn't bode well'
Steve Chambers, from the Campaign For Better Transport, said he was concerned about the disruption seen on Sunday.
"The changes have been brought in on a day when there are usually less passengers and less trains and still there have been problems," he said.
"It doesn't bode well for tomorrow. But the biggest issue altogether will be people turning up to get their usual train and finding it no longer exists.
"The way customers have been informed just has not been good enough."
The RMT also claims passengers with reduced mobility may be left behind if a train is at risk of delay.
GTR said it placed high priority on making its services accessible to all.