Virgin Trains confirmed that half its services leaving Manchester Piccadilly for London were cancelled, with one train leaving every hour instead of the scheduled two.
The services that were maintained were diverted to Birmingham, adding with 30-35 minutes to journeys.
All Virgin trains between London, Manchester, Liverpool and Scotland were affected.
With each train capable of accommodating 450 people, it is thought thousands of people were affected by the disruption.
The problems were caused by apparent fire damage to trackside cables feeding overhead electricity cables on the West Coast Mainline near Rugeley, south of Stafford.
A spokesman for Virgin said police suspected an arson attack.
Engineers were looking at the problem and it was hoped services could be back to normal by this afternoon. He said: "It is a suspected arson attack at Rugeley. We don't know the precise time of the attack but it was some time overnight.
"It's caused a lot of disruption and we are having to divert the Manchester, Preston, Liverpool and Glasgow services via Birmingham.
"In Manchester we are having to run an hourly instead of a half-hourly service. We expect there will be disruption most of the morning and we are asking people to be patient while we try and get things back to normal."
Four services from Manchester had been cancelled early this morning and more trains were likely to be axed.
"There will be more services lost during the morning undoubtedly," said the Virgin spokesman.
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I had a rail journey from hell, yesterday, thanks to the arsonists. I don't suppose anyone will be brought before the courts. Even if they were, I expect their defence would be that is was 'a cry for help'. They would probably be sent on a cruise by do-gooding magistrates.
I was also caught up in this chaos yesterday on the 17.45 out of Manchester Piccadilly. However the whole incident was dealt with as best as possible. There was much information around Manchester Piccadilly about the delay, so I knew before I got on the train. The train manager was also very helpful during the course of our journey. I arrived at Milton Keynes Central an hour late which didn't really bother me.
My friend made a journey from Preston to Milton Keynes today (Friday) and has spent 6 hours travelling, a journey which should take 2 hours maximum. I think there was a derailment near Preston which caused this upset to the system.