The Government shelved plans for major improvements in June after Network Rail admitted it had been “overly optimistic” about completing a five-year, £38 billion plan.
Transport Secretary Patrick McLoughlin responded by announcing that the plan was being “reset” because it was “costing more and taking longer”.
He said electrification work was being “paused” on the Midland mainline and on the Transpennine route between Leeds and Manchester.
The decision was made after the Government received an assessment of the state of major Network Rail projects.
The DfT has now refused a Freedom of Information Act request from the BBC to release that assessment, even though it acknowledged there was a “public interest” in the document.
The department told the broadcaster the assessment would remain confidential because ministers and officials were still making decisions about the future of rail upgrades.
“While we recognise there is public interest in the detailed assessment of Network Rail’s cost and delivery schedule, policy proposals are still being carried out and this information forms part of that process,” the department’s response said.
“The information is a critical input to the proposals on how the rail upgrades programme will cost and be delivered. Ministers and officials need a free space in which to carry out rigorous assessment of the re-plan.”
The department also refused to release any correspondence with Network Rail that could show warnings of problems so serious they might lead to the pause in electrification, claiming it would cost more than the £600 limit in the Freedom of Information Act to comply with the request.
Labour has accused the Government of “cynically” hiding problems with the electrification programmes from voters during the general election campaign.
The Opposition has claimed ministers were aware as early as last March that “deferrals” to improvement schemes would be required in the weeks following the election.
But Mr McLoughlin has insisted that he was only told there needed to be a pause a week before he made his announcement in the House of Commons.