Ministers hatched a secret plan to dramatically scale back the biggest rail investment programme in a generation and approved cuts to major infrastructure projects – despite being warned this would severely damage the overall benefits of the scheme.

Sensitivity about the £1 billion Edinburgh Glasgow Improvement Programme (EGIP) persuaded the Scottish Government to commission a consultancy to privately advise on how "substantial" savings could be achieved – while keeping the main players, Network Rail and ScotRail, in the dark, the Sunday Herald has learned.

But, weeks after £350 million was cut from the flagship programme, senior figures in the industry are questioning the work carried out by Jacobs, an international transport consultancy, claiming the consequences have not been properly thought out.

The revisions included jettisoning about half the envisaged electrification of central Scotland's rail network, with lines to Stirling, Alloa and Dunblane now slated for a later phase – the timetable for which is yet to be laid out – but the main Edinburgh-Glasgow via Falkirk route is still due to get overhead wires.

Major projects such as the Dalmeny Chord – which would allow Glasgow trains to switch on to Fife lines outside Edinburgh and give access to a new tram interchange at Gogar – have been cut, alongside grade-separated junctions at Winchburgh and Greenhill which would allow trains to pass on separate tracks.

When he announced the revised scope on July 4, Transport Minister Keith Brown said this was due to "changed circumstances", which meant the benefits of EGIP could be delivered at a far lower cost.

Instead of running an extra two trains an hour between Glasgow and Edinburgh on the main line via Falkirk, the current timetable of four trains an hour would be retained, but with extra carriages to increase seat numbers.

However, the Jacobs report, which was commissioned in May but has only been seen by a handful of people in the industry, makes clear that the purpose of the change in scope was to save money.

Sources said officials at Transport Scotland (TS) instructed Jacobs to see if "substantial cost savings" could be achieved while retaining EGIP's key outcomes and to examine if all work packages were necessary.

In response, Jacobs briefed TS that the main elements were "essential" to delivering the benefits the programme was supposed to deliver and could not be removed without a "major reduction" to these benefits. The only possible exception was the electrification of routes in Stirling, Alloa and Dunblane, it found.

But the consultancy concluded that no serious work had been done to see if longer trains could be operated on the main Edinburgh-Glasgow line and proposed this as a solution to cutting back on the specification of the programme.

One source claimed that one consequence would be that services from Glasgow to Cumbernauld were likely to take longer as the route would have to accommodate electric services on the same line as slower diesel trains travelling onwards to Stirling. "Did Jacobs do the timetabling work? We suspect not," the source added.

Another source said there was "no detail" provided when the scope of EGIP was changed. "We're now having to find the detail," he said. "You're still going to get pinch points on the network because the only way to remove those is to have grade-separated junctions [which now will not be built]."

The same sources were puzzled by the official budget as they estimate the elements left in the scheme would cost around £400m to deliver – far below the £650m touted by officials. "Either they want to announce that they've achieved further savings later on or they're going to put things back into the project," one source said.

A TS spokesman said it had commissioned Jacobs to review whether the original proposal of six trains per hour was necessary and whether alternatives could provide similar benefits, claiming the resulting report was "technically competent and robust".

He added: "The EGIP timetable is based on a network of diesel and electric services across the Central Belt. We continue to work with ScotRail and Network Rail to ensure robust contingency plans are in place."

BEHIND THE SCENES

It was boldly hailed as "on time and on budget" seven years before its scheduled completion in 2016, but nearly three years later, confidence that the £1 billion EGIP would repair Scotland's reputation for delivering major transport projects has foundered.

Part of the early confidence stemmed from a belief that track owner Network Rail had patched over a difficult relationship with Transport Scotland (TS). But, after conducting one of the biggest public consultations on a transport scheme ever held in Scotland, Network Rail was then cut out of the process of reviewing the scheme.

TS, ScotRail and Network Rail all insisted that the Jacobs review had been shared between all three prior to being confirmed, although the Sunday Herald has been told that this happened only days before the official announcement. Moreover, officials at NR and ScotRail were still being updated on in the following days.

David Higgins, Network Rail's chief executive, said the company had been aware of the review and was involved in "reviewing" the process.

"We remain committed to continuing our work with our partners to deliver EGIP which will be a hugely significant step in the process of improving the railway in Scotland, and will bring real benefits to the public."