Cable thieves has left Olympic travellers and commuters stranded for up to 90 minutes on the eve of the Games, as they headed for London on First Capital Connect trains.
A FCC spokesman called the delays "absolutely devastating" and said they working hard to stop normal services, but the theft "could not have come at a worse time."
The theft led to signalling problems at Bedford, meaning other train services did not stop at the station.
The trains, which run through central London between Brighton and Bedford, carry around 75,000 people a day, but were running only one third of their normal services on Thursday morning.
Trains were suspended between Bedford and Luton.
The FCC spokesman said: "Today is going to be extremely difficult for our passengers, our regular commuters and visitors to London."
A National Rail spokesman said: "A signal fault between Luton and Bedford caused by attempted cable theft - a mindless and despicable act - is resulting in significant disruption to FCC services in the Bedford area this morning."
The theft occurred before midnight on Wednesday but engineers were unable to restore the service in time for the Thursday morning rush hour.
Cable theft is estimated to have cost the tax payer £18.3 million last year and rail companies are urging legal reforms and harsher penalties for the thieves.
Canary Wharf station on the Underground's Jubilee line in London's Docklands was shut due to a fire alert on Thursday morning.
Passengers had to leave the station - one of the busiest in London. Jubilee line trains were running normally but were not stopping at Canary Wharf.