The project, which this week was included in the Edinburgh to Glasgow Improvement Programme, is due to be finished by March 2019.
The initial plan to run extra trains out of Queen Street on the new electrified line was abandoned last year in favour of running longer trains to take more passengers.
That means creating longer platforms but because there is a tunnel to the north, it means they can only be lengthened southwards towards George Square and West George Street, which means a remodelling and rebuild of the entire station.
This and other work to connect the station to Buchanan Galleries and public realm work increased the cost from £48million to £120m.
The overall cost of the EGIP plan has now gone up from £650m to £742m.
Electrification will start along the route via Falkirk High station first and then the construction work on the station will start in 2016 and last three years.
Full detailed plans of how the work will impact on other services and on the travelling public are to be revealed later by Network Rail.
There are concerns over some local services when platforms have to be closed to allow them to be lengthened to accommodate the new eight-carriage trains.
There will be fewer trains and services in and out of the station during the construction phase as the capacity will be reduced for a period as the current seven platforms will not all be available during re building.
Full details on the level and length of disruption to the public, access arrangements and alterations to services are awaited from Network Rail in the near future.
No details have yet been released on whether there is a need for the station to be closed and if so, for how long.
Some services are expected to be required to be re-routed via the low level station or some via Central Station, which will again have a knock-on effect on the services currently run on the Argyll line, busy with commuters travelling to work in Glasgow from Lanarkshire, and Dunbartonshire.
The business case states: "The detailed timetabling has identified areas where there may be knock on impact on some non-EGIP service."
IT continues: "This is common in major infrastructure works, however work is currently being undertaken to minimise and eliminate these disbenefits."
The work is intended to make the passenger experience at Queen Street better, but the report is unable to explain exactly how.
It states: "The redevelopment of the station will be likely to deliver additional benefits which have not been captured in this analysis."
It says passengers will enjoy the "ambience" of a new station.
It states: "The redevelopment of Queen Street will generate significant benefits to the public realm given the station's position on the corner of Glasgow's iconic centrepiece, George Square."
The Queen Street work will mean demolition of the SPT headquarters at Consort house and the bar in West George Street.
Part of the Millennium Hotel will also have to be removed for the new frontage and it is expected other property in the surrounding area for the connections to Buchanan Galleries will need to be purchased.
The EGIP work is due to deliver the electrification of the route by December 2016.
Other stations and depots work by December 2016 and Queen Street completed by March 2019.
The overall Queen Street project involves converting the current Buchanan Galleries car park in Cathedral Street to the extension of the shopping centre.
A new car park will be built on the current taxi rank to the east of the station at North Hanover Street.
A series of walkways will be created connecting the station with the shopping centre, car park, and Buchanan Street.
Transport Minister Keith Brown said: "Since I announced the first phase of EGIP in July 2012, we have further developed the original scope to include an even greater transformation of Glasgow Queen Street Station and I am pleased to announce the publication of the EGIP Business Case, which takes that into account.
"This prudent and comprehensive assessment of the investment case for EGIP demonstrates substantial benefit for Scotland and its rail users and that the first phase can be delivered on time and on budget."
It is expected that with electrification the current journey times between Glasgow and Edinburgh of around 52-55 minutes will be reduced to 42 minutes by 2018.
The longer trains are designed to relived congestion at peak times on the route and improve reliability as the latest data in the report shows almost one in five trains on the line are late.
Transport Scotland said the work will deliver a cleaner, greener, quieter railway with lower carbon emissions,improved capacity and more seats with less crowding at peak journey times.