The engineering works that caused chaos on the main rail route between Birmingham and London overran because too many contracting groups were taken on by Network Rail, a union has claimed.
The company said services would be running normally on the West Coast main line from 5am this morning.
Transport union TSSA said the inquiry into NR's failure to meet deadlines on the work at Rugby station should examine why nine different firms were involved with the £400 million track and signalling project.
Gerry Doherty, the union's general secretary, said: "We think the number of firms involved may well have been a recipe for confusion.
"The inquiries by the Office of Rail Regulation and NR should examine the precise role of the private contractors and whether their roles were properly defined and managed. It may well be that too many cooks spoiled the broth."
Network Rail confirmed that nine different contractors had been working on the project, but said it could not comment on the allegations.
And it added it would be looking forward to the results of an enquiry it was carrying out to see what had happened.
A spokesman said: "At the moment our focus is on getting the railway reopened. We are very keen to understand how it happened and will be taking a very thorough look."
Network Rail yesterday apologised for "mucking passengers around" over the engineering work, and said the full service would be running again this morning.
Chief Executive Iain Coucher said yesterday: "I can confirm that trains will start to run normally on the West Coast again from tomorrow. I can take no comfort from this news in the knowledge of the pain and inconvenience we have caused passengers over the past few days. I know that we have let passengers down with the over-run at Rugby.
"An investigation into the causes of the over-run has been launched and I will be chairing a high-level meeting next week to review what's happened.
"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."
NR was roundly condemned by opposition MPs, passenger groups and businesses over its handling of the festive engineering work, which saw a further 60,000 passengers face delays of two hours or more yesterday.
The engineering work was supposed to have finished on New Year's Eve, but continued for three extra days.
The Office of Rail Regulation ordered an investigation into the matter after complaints from Virgin Trains, the company that runs the main West Coast Line routes.
It hinted Network Rail could be facing a hefty fine if it is found to have breached its contract with the rail route operators. Last year the company was fined £2.4 million after signalling work overran at Portsmouth station.
And Network Rail will face a compensation bill to reimburse Virgin for the thousands of passengers who cancelled or moved journeys because of the problems.
Passengers facing difficult journeys after the engineering works carried on into the new year were further angered by the disruption coinciding with above-inflation train fare rises taking effect.