Concerns over the work which will see extended platforms, the building of a new glass frontage and the demolition of the Consort House office block and part of the Millennium Hotel, have been raised by city transport bosses.
Officials at Strathclyde Partnership for Transport (SPT) have raised a number of points they fear will cause problems for rail users.
Worries over the lack of taxi space and disabled parking at the station, as well as concerns over the route of the new Fastlink service, have been raised.
It is also considered 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 Buchanan Galleries, as part of a re-development of the mall, with walkways and car parks connected to the station.
The re-modelling means there will also be more shops in the station.
Jim Coleman, SPT chairman, said: "With Buchanan Galleries, the station works, the hotel demolition, all in the one area, being done by different organisations, 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 redevelopment of Queen Street provides an opportunity to significantly improve integration between this major national, regional and city transport hub, its surrounding city centre land-uses and the wider transport network.
"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.
The current taxi ranks, in the car park at North Hanover Street and at Dundas Street, both offering direct access to the station concourse, are being removed and a new rank will created on the south side of West George Street, meaning access for disabled and elderly passengers, and those with heavy luggage, is not from the pavement and passengers will have to cross a road to reach the station.
Concerns about the development's impact on the surrounding road network have also been raised.
The station is one of the key transport interchanges which will be served by the new Fastlink bus service.
The priority bus route will pass the front of the station, on George Square, and up North Hanover Street to Buchanan Bus Station.
However, with Fastlink due to be complete in 2015, and the station and galleries work not fully finished until 2019, there are fears work will disrupt the full operation of the new bus service.
Major demolition work will be taking place on the Fastlink route, with Consort House and the Millennium Hotel extension being pulled down before the station is rebuilt.
Charles Hoskins, SPT director of projects, told councillors there would be implications for Fastlink.
Network Rail said the station will have more entrances, lifts, ticket gates and six disabled parking spaces, compared to three at present.
There will be a taxi drop off point in the new car park and a taxi rank is still being considered.
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.
"The redevelopment will significantly enhance the concourse area and retail facilities, double the number of disabled parking spaces, double the number of step-free entrances, more than double the availability of cycle racks and increase the number of ticket gates and lifts."