Ministers were understood to be concerned over SPT's ability to deliver the scheme on time and to budget after it experienced delays and cost overruns on its Partick Interchange scheme.
Announcing the change of authorised undertaker on Friday, Scottish transport minister Stewart Stevenson said: "As with all infrastructure projects , funded from the public purse, the overriding objective must always be to deliver as effectively and as efficiently as possible.
"This represents the right way forward for GARL, a nationally significant project vital for the local and wider Scottish economy and in capturing the full benefits of the 2014 Commonwealth Games."
Although some comment from un-attributed industry sources in the Scottish media said that there were design problems with the scheme, which includes 2km of new railway between Glasgow International Airport and Paisley St. James, this was denied by SPT personnel.
SPT chief executive Ron Culley said: "GARL now needs to be built so the time is right for Scotland’s national transport agency to take it forward through the implementation stage."
The scheme is currently due on site in 2009 with operations beginning in 2012, well before the July 2014 Games. The scheme includes upgrading of the 9km of route between Paisley Gilmour Street and Glasgow Central as well as the new railway.
In the nine years since devolution the Scottish Government has obtained further powers over the rail network and services and established the national transport agency in 2006. By contrast SPT, formerly SPTE, has lost powers notably in losing its co-signatory role in regard to the passenger franchise.
Just two weeks ago SPT assistant chief executive John Halliday told delegates at NCE’s Scottish Transport Engineering conference that: "We expect to award the design and build contract for the new section of railway, which includes a 142m single span bridge over the M8, 1300m of viaduct and 300m on embankment, in February 2009."