Train passengers were unable to buy tickets online with several operators or a major retailer due to technical glitches.
Among the companies who reported being affected by problems on Tuesday morning were Greater Anglia, Northern and Southeastern.
Trainline, the UK’s largest train ticket retailer, was also hit by a fault.
The rail industry source told the PA news agency that companies suffered “different, unrelated technical issues”.
Greater Anglia and Northern said passengers could not make card payments on their apps or websites, while Southeastern warned that ticket-buying at stations was also affected.
Northern posted a message on Twitter at 8.14am which stated: “We are aware of an issue with our app/website whereby customers cannot complete their booking.
“This is being looked into and we hope to see a fix soon.
“In the meantime please use ticket buying facilities at stations to purchase your tickets.”
In an update posted at 11.22am, it wrote: “Issues with our app/website have now been resolved, customers are able to purchase tickets as normal.
“We are sorry this has affected our customers this morning.”
Trainline told customers that its booking system was “experiencing a technical glitch”, before later stating that “all booking services are back up and running”.
The Rail, Maritime and Transport union, which has claimed there are plans for a mass closure of station ticket offices, tweeted: “Numerous train operating company ticket purchasing apps, and Trainline, are down this morning.
“This merely highlights the short-sightedness of Government plans to close up to 1,000 ticket offices.”
A spokesman for industry body the Rail Delivery Group said: “We are aware that customers have experienced problems purchasing tickets for trains operated by a number of train companies today.
“We apologise for the inconvenience caused.
“In some cases, the problems were resolved by mid-morning and customers should be able to buy tickets as usual.
“We are working with the companies to fix the remaining technical issues.”