Transport Minister Keith Brown announced the cuts to the £1 billion Edinburgh Glasgow Improvement Programme (EGIP) in July following a secret review undertaken by independent transport consultancy Jacobs.
However, following a Freedom of Information (FOI) request from The Herald, Government agency Transport Scotland has admitted the Jacobs report had not been completed by then and was still in "draft" form.
The programme, cited by ministers as evidence of their capital investment-led economic growth strategy, was intended to provide an additional two trains an hour on the main Glasgow-Edinburgh line and electrify the route, along with lines to Stirling and Dunblane.
But about half of the electrification programme has been postponed and the current timetable of four trains per hour will be retained between Glasgow and Edinburgh, but with more coaches per train.
The cuts provoked disquiet in the rail industry amid fears the mix of diesel and electric services in the central belt will lead to worsening train delays on Scotland's busiest routes.
In response to The Herald's application, David Ray, EGIP's project sponsor at Transport Scotland, turned down the request, saying an exemption applied under FOI legislation.
He wrote: "This is because the information you have requested relates to material, ie the Jacobs report ... remains in draft form and is therefore still in the course of completion. We expect to publish it in its final form within the next two months."
Mr Brown has also confirmed in response to a parliamentary question that Jacobs did not discuss its review with either train operator ScotRail or Network Rail, which is carrying out EGIP on behalf of the Scottish Government, a claim first reported by industry sources in the Sunday Herald in July.
Labour has called on Mr Brown to provide an urgent statement to the Scottish Parliament, claiming the timing of the announcement over the recess had prevented any discussion.
Transport spokeswoman Elaine Murray said it "beggared belief" the report was only in draft form. She added: "If that is the case, and it wasn't discussed with ScotRail, Network Rail or any councils, there is all the more need to have a discussion in Parliament about these decisions."
LibDem transport spokesman Jim Hume said: "This is beermat policy-making at its finest. The SNP Government has slashed £350m from EGIP's budget and has based those cuts on the findings of a report which hasn't even been completed, let alone published."
Alex Johnstone, for the Conservatives, said: "This is yet another example of the SNP rushing headlong into decisions based on data that no-one has seen, and isn't even complete yet.
"Thousands upon thousands of people were anticipating these improvements, and they deserve to know why they have been scaled back."
A Transport Scotland spokeswoman said: "Transport Scotland engaged Jacobs Consulting in May with a specific remit to review and assess whether the original proposal for six trains per hour delivered the EGIP outputs and to identify and review alternative options that could provide similar benefits.
"Jacobs Consulting reported back to Transport Scotland and Ministers with their findings, which were fed into the finalised EGIP plans to ensure the most beneficial and cost-effective way forward.
"Those findings are now being prepared for publication, for example by removing commercially confidential information, and will be published shortly."