Damage to overhead electric wires is causing severe disruption to train services between Bedford and London St Pancras.
The problem, near Luton, has blocked two of the four lines on the route, resulting in commuters using Thameslink and East Midlands Railway being hit by delays and cancellations.
Network Rail engineers are working to repair the wires but disruption is expected until the end of service on Thursday.
A spokesman for the Government-owned company said: "We apologise for any inconvenience this disruption may cause.
"We are working hard to resolve the issues as fast and as safely as possible.
"We thank you for your patience and understanding as we carry out this emergency work."
Other routes affected include Gatwick to London via Redhill, East Grinstead to London, and Littlehampton to London.
Thameslink said journeys could take up to an hour longer than normal.
The operator added: "Trains that are running will be very busy so you might also wish to travel on an alternative route."
Jenny Saunders, customer service director for Thameslink and Great Northern, apologised for the delays and cancellations.
She said: "Network Rail will repair the damage as quickly as possible but disruption is currently expected to last all day.
"It's not an acceptable service that we are delivering for our passengers this morning and it is imperative that Network Rail and Thameslink continue to work together over the coming weeks and months to understand what is happening when incidents like this cause disruption."
She added that passengers delayed by at least 15 minutes should claim compensation.