Transport Scotland has been told the seven-year gap between the electrification of the Glasgow to Edinburgh line and a proposed high speed link between the cities does not justify the spend on Glasgow's Queen Street Station to accommodate longer trains.
Strathclyde Partnership for Transport (SPT) wants more detail on the revised Edinburgh to Glasgow Improvement Plan (EGIP) which has been cut in cost from £1.2 billion to £650 million to allow it to measure the impact on commuter services into Glasgow.
In a report to go before an SPT meeting it was suggested a phased redevelopment of the station is thought to be more compatible with high speed rail to avoid over provision between the cities.
The initial EGIP plan was to see more trains running on the line with increased frequency between Queen Street and Edinburgh.
When that was abandoned and the programme costs slashed from £1.2bn to £650m the plan was to run longer trains.
SPT said one platform can take eight carriages and the others can take seven which would reduce overcrowding at peak times.
The new electric trains expected to be used on the line are able to run using seven carriages.
SPT notes that in 2016, two years before the station work is completed the service will be delivered using seven car trains.
Jim Coleman, SPT chairman, said: "I see no logic to the planned overhaul of Queen Street Station and how this will fit with a longer term commitment to a high speed rail network. The level of chaos this will cause just a few years before further big changes are potentially necessary just doesn't make sense."
A Transport Scotland spokesman said: "EGIP forms part of a wider £5bn investment package in Scotland's railway infrastructure, rolling stock and services, and is the next step of the Scottish Government ambition to electrify our railway network.
"The redevelopment of Glasgow Queen Street Station will transform the passenger experience, enabling existing platforms to be extended to accommodate longer trains and maintain currently timetabled services.
"The planned improvements to one of Scotland's key rail stations is essential to meet passenger demand on the Edinburgh Glasgow via Falkirk high route, which we expected to exceed available capacity by the end of this decade, and including the redevelopment of Queen Street Station will future proof capacity on this critical route.
"High Speed rail is a longer term objective and when introduced will add to the opportunities for travel between Edinburgh and Glasgow and meet future passenger growth."