National Rail says a “countrywide fault” has caused major disruption to at least 10 lines of the UK’s rail network.
National Rail blamed the problem on the radio system used between train drivers and signallers.
The issue has now been resolved, but residual delays may continue until the timetable is restored.
Services in and out of England’s major transport hubs including Manchester Piccadilly, London Paddington and Southampton Central were affected.
Great Northern, Northern, ScotRail, South Eastern, Southern, South Western Railway, Thameslink, Gatwick Express, Heathrow Express and Elizabeth Line were all affected.
Travel expert Simon Calder told BBC Radio 5 Live that Friday morning was “a bad rush hour for a lot of people”.
National Rail said the issue appears to be a fault with the onboard GSMR radio system, which is used to communicate in emergency situations.
The BBC understands that the cause of the error has been found and fixed.
Previously, to minimize disruption, a backup system was being used instead.
Network Rail said the problem was mainly affecting trains at the start or end of the day, with a spokesman saying “there are delays of a few minutes at the start of the day”.
But “once up and running the system is operating normally and the impact on passengers is minimal,” he added.
Although the issue has now been resolved, National Rail said there may be some residual disruption while timetables are restored.
It advises that passengers may be entitled to compensation if their journey is delayed.
‘Third day in a row’ of delays
One passenger told the BBC he paid £54 for a taxi ride to finish his journey.
Matthew Smith, 47, was traveling from Portsmouth to Basingstoke for work on Friday morning. The train he intended to catch was no longer stopping at Basingstoke so he was advised to catch the next train half an hour later.
“The station staff had as much information as I could get from the app,” he said.
Mr Smith caught a train to Hevant before deciding to end his journey in a taxi.
“This is the third day in a row that these trains have had problems and it is not pleasant or acceptable especially given the price we pay for rail travel,” he said.
In London Waterloo, some commuters said the disruption would delay them to work by at least an hour. A woman said she was running three hours late for a job interview.
BBC producer Caroline Rice was on the train from Southampton to Waterloo, but it ended at Woking an hour behind schedule.
This was on top of the disruption caused by the enormous amount of engineering work.
Across the network on Friday morning, most delays were no longer than 15 minutes, but some services were delayed for up to an hour.
Earlier in the day, National Rail said passengers should plan for some services to be canceled at short notice.
ScotRail said its services were affected on Friday morning but have since returned to normal operations.
The Gatwick Express was only running between London Victoria and Gatwick Airport, and some Heathrow Express trains were delayed.
Services along the entire Elizabeth line were also affected.
Elsewhere, journeys between Brighton and Southampton Central, and King’s Lynn and London King’s Cross, were not running the full length of the line.
What is the cause of the disturbance?
This problem happened due to GSMR system of Railways. which allows drivers and signalers to communicate in areas – such as tunnels – where previous analogue systems did not work.
It works like a mobile phone, but the digital system does not rely on commercial mobile phone operators. The rail network has its own telephone and mast system.
A rail source told the BBC that “the system [wasn’t] Connecting easily.”
The BBC understands that a new piece of hardware installed as part of a system upgrade at a major telecommunications hub in Stoke was the source of the problem.
The replacement hardware is installed and the system is rebooted.
While it was being fixed, we were told there was no significant safety issue, as staff were using a workaround to manually reconnect.
This is a well-practiced backup where drivers enter a code provided to them on a “wild card”, which allows them to establish connections with the national network.
This is described to us as working like a Wi-Fi password – when the correct code is entered, the system is fully activated and will remain so.
Radios that were manually programmed by drivers are now reverting to automatic mode.