Network Rail has said the Government was informed before the election that major rail upgrades could need to be put on hold, appearing to contradict claims by secretary of state Patrick McLoughlin.
Mr McLoughlin said he first received advice that major programmes should be paused on 15 June after the election.
In a letter to the shadow transport minister Lillian Greenwood, Network Rail chief executive Mark Carne states: 'In mid-March 2015, Network Rail informed DfT that decisions may need to be made in the coming months about the deferral of certain schemes.'
Ms Greenwood accused ministers of having 'covered up the extent of Network Rail's problems for months'.
'There are serious questions to answer over the conduct of senior Conservative politicians who promised to deliver vital electrification projects during the election, only to then shelve them once the ballot boxes had closed. The Government's insistence that it was unaware of the extent of these problems is becoming less believable by the day.
'There can now be no doubt that ministers knew that important projects faced the axe, but they chose to mislead voters in the Midlands and the North instead of admitting the truth. We need to know the true extent of the black hole in Network Rail's budget because other important projects are also at risk of being 'paused' or cancelled outright.'
Documents that could reveal the scale of the delays and cost overruns on Network Rail’s major upgrade programme are being kept hidden by the Department for Transport, it has also emerged.
The BBC reports that a Freedom of Information request made by its journalists was refused by the department, following the electrification of the Trans-Pennine and Midland main line routes being put on hold in June.
Ministers made the decision having been given an assessment of the major projects programme, which civil servants told the BBC would remain confidential because ministers and officials were still making decisions about the future of the upgrades.
In response to a letter from the opposition to Patrick McLoughlin, the secretary of state said: ‘The government remains committed to the £38bn investment through Network Rail and the vital benefits that rail enhancements will provide for passengers.'
He added that he had been open about "very significant challenges" to the programme in December last year.