The West Coast route has reopened after overrunning engineering work caused major disruption.
Virgin has said passengers can claim compensation
Network Rail could be fined millions of pounds by regulators after tens of thousands of travellers were affected.
The company has said it wants the project managers and principal contractors to explain why the work at Rugby was not completed on time.
But it has denied newspaper reports it is planning to bring maintenance work back in-house.
The Times said Network Rail was "likely" to end the use of contractors to oversee rail renewal projects.
The company issued a statement on Thursday saying that chief executive Iain Coucher will chair a "high-level" meeting next week on the issue.
He said: "I will be summoning our project managers, Bechtel, and the principal contractors involved to attend so they can personally explain to me what has gone wrong.
"They gave me assurances before Christmas on which they have not delivered. I want answers from them."
Scotland to London services were due to return to normal on New Year's Day but staff shortages meant work was delayed.
Works at Rugby shut the line between Birmingham International and Northampton, prompting Virgin to advise passengers not to use its trains.
Mr Coucher said an investigation into the causes had been launched and admitted Network Rail had "let passengers down".
He said: "The railway will be back tomorrow (Friday) but the work is far from done.
"We have a significant programme for developing and expanding the railway over the coming years and we have to make certain that it is carried out to plan."
Rail Regulator Chris Bolt said Network Rail had been fined £2.4m last Christmas following signalling problems at Portsmouth.
"That is clearly a precedent we have already put in place, so fining them again, if that will help to resolve these problems, is something we won't hesitate to do," he said.
More people had been affected by the more recent problems than at Portsmouth, he added.
"It's too early to say what the fine might be but it clearly could be substantial," he said.
Network Rail's operations director Robin Gisbey said a "planning error" had resulted in not enough overhead wire electricians being asked to come to work, admitting: "We got it wrong."
He added: "We've now got extra resources into Rugby, we've been flat out over the last couple of days."
Chris Gibb, managing director of Virgin Trains, said "very few" passengers had been using its service.
He added: "What I want to see is a change in behaviour by Network Rail to ensure this never happens again.
"I want to be able to provide a good service to customers, I want to know in advance when the engineering work is going to take place and not be told at the last minute."
The company's chief executive Tony Collins said: "This has been a fiasco and our customers expect and deserve better."
Meanwhile, Virgin has announced that saver fares will be available on all trains, including peak services, next Monday and Tuesday to enable customers to travel for less at short notice.
It also said passengers could claim compensation if their journeys had been affected.