An urgent inquiry is to be carried out into engineering work delays which have caused chaos for thousands of people.
Many people were expected to return to work on Wednesday
The Office of Rail Regulation began the inquiry after West Coast Mainline work overran by two days.
The works at Rugby have left the line closed between Birmingham International and Northampton and Virgin has advised passengers not to use its trains.
London's Liverpool Street station was also closed on Wednesday due to overrunning works but has now reopened.
The railway terminal opened to passengers on Thursday morning, a day late, after being closed for 10 days for work on a bridge and overheard cables.
Virgin said passengers could claim compensation if their journeys had been affected by the West Coast Mainline delays.
Network Rail apologised for the delays and said it was working "flat out" to restore normal services.
Chris Gibb, managing director of Virgin Trains, told the BBC that Network Rail said the line around Rugby station would not reopen until 0500 GMT on Friday.
Birmingham International station was also forced to close on Wednesday morning after a small fire broke out. Nobody was injured.
The regulator's inquiry could lead to sanctions including a financial penalty.
Rail regulator chairman Chris Bolt said: "We fined Network Rail for its project planning and management failings after it failed to complete the Portsmouth re-signalling project last Christmas.
"It is extremely disappointing to have a repeat of that experience on key parts of the network."
Network Rail has apologised to passengers for the disruption caused by the "unacceptable" overrun.
A spokesman said the "critical issue" was a shortage of specialist engineering staff, but additional manpower had been drafted in and was working hard to restore the services as quickly as possible.
Operations and customer services director Robin Gisby said: "Both these overruns are completely unacceptable and an urgent investigation into what has gone wrong has been launched."
The delays come as train passengers across the UK face above-inflation fare rises of up to 11%.
Regulated fares, which include most season tickets, are going up by an average of 4.8%, and many unregulated fares are set to rise by much more.
Consumer groups said the rises were unjustified, but train operators said they were needed for improvements.
Rail operator Virgin said it was exasperated about the West Coast Mainline delays and advised its passengers not to travel.
Mr Gibb said: "This is a major inconvenience to tens of thousands of our customers returning to work and it is not acceptable."
Replacement bus services were being provided between Birmingham, Coventry and Northampton, but they were expected to add two hours to journey times.
The work had originally been expected to be finished by New Year's Eve, as Network Rail had been hoping to complete the works over the festive period when there were fewer passengers.
Virgin had already lodged a complaint with the rail regulator after Network Rail announced on 21 December that the works would run into New Year's Eve.
Passengers to and from London are being urged to use alternative routes as follows:
- Birmingham - Chiltern Railways to Marylebone
- Nuneaton - Cross Country/East Midlands Trains via Leicester to St Pancras
- Rugby - Drive to Kettering then East Midlands Trains to St Pancras
- North West England - Trans Pennine Express/East Midlands Trains via Sheffield to St Pancras
- North Wales - Virgin Trains/Cross Country/Chiltern Railways via Birmingham to Marylebone
- Scotland - National Express East Coast to King's Cross
You can read a selection of readers' comments below:
As an employee for Virgin Trains, I would hope that passengers realise that the delays have been caused by Network Rail not completing engineering works and not by Virgin Trains. Far too often, people see delays on the railways and automatically blame the rail operator which in the majority of cases, it is not.
Jack, Manchester, UK
Our three children are trying to return from Stoke on Trent after visiting relatives and are now stranded. We have been given conflicting information from the travel phone line and both Virgintrains.com and national rail website are telling us they can get back as normal via Euston. They need to update their websites and give accurate information. We have been told the children will have to travel to Stockport, then Sheffield then to London St. Pancras. Where do we go from here?
Kay Instrell, Nottingham, London
A planned break to London with the kids (to see a show etc) is now disrupted. On deciding to use the train I pre-booked my tickets three months ago (but was not guaranteed a seat). The journey was meant to be 1hr 40 mins but becomes a 45 min train journey, an 1 hr 30 mins bus journey followed by a 1 hr 30 mins train journey (although this is subject to delays). On applying for a refund I am told it takes up to 21 days (it only took five minutes to take the payment) and is subject to a £10 admin fee. I am now taking the car and the kids ask why?
Adrian, Lichfield, UK
I have been affected by the closure of Liverpool Street which delayed my journey to work. I think the compensation offered for this sort of disruption is too low and the procedure to get it far too complicated. Local stations should be able to provide compensation on the day etc.
Alison Cook, Wickford, Essex
I was forced to get a taxi from Wolverhampton to Sandwell costing £34 Due to these delays.
Luke, Wolverhampton UK
I booked my tickets well in advance to get a train back to work in London on the 2nd of Jan. This has meant having to take a day as holiday but I felt this would be necessary at the time in order to avoid the usual nightmare of having to travel back from Carlisle on the 1st of Jan. However it looks like it was a waste of a days holiday. It is all well and good that Virgin advise people to travel via alternate destinations however I have no option as I cannot afford a new ticket and apparently the other train operators will not accept the value advance ticket which I purchased, meaning I'm being punished for having bought my ticket well in advance.
Michael Wood, Carlisle, Cumbria