Officials at Strathclyde Partnership for Transport (SPT) have raised a number of concerns about the work - which will involve extending platforms, building a new glass frontage and demolishing an office block and part of a hotel.
It is claimed the redevelopment puts the provision of shops above the needs of passengers at Scotland's third busiest station.
The work will link the station to the Buchanan Galleries shopping mall, and the re-modelling means there will also be more shops in the station.
SPT chairman Jim Coleman said: "There are still huge questions over these plans. The travelling public is going to suffer when this kicks in.
"The main problem is there is a lack of co-ordination between three or four developments. The station will still be open and people using it, but the place will be a quagmire of demolition."
In a report to councillors, Eric Stewart, SPT's assistance chief executive, said: "The plans produced to date only partially develop this opportunity and appear to have a potentially disproportionate focus on commercial/retail provision, with an estimated increase of more than 60% of commercial/retail floorspace. This appears to be at the expense of station passenger facilities and optimum integration."
SPT has objected to some of the plans, including limitations within the station and lack of integration with other modes of transport.
However, Network Rail said the station would have more entrances, lifts, ticket gates and six disabled parking spaces, compared to three at present.
A spokesman said: "We are confident the redevelopment of Glasgow Queen Street will transform not only the building but also passengers' experience of using the station, offering the high level of facilities and amenities appropriate to a 21st-century station."