The RAF's aircraft display team traditionally use the red, white and blue of the union flag during their fly pasts.
Proposals for an exception to be made for Wednesday's event were eventually ditched, but not before they had appeared in an official media guide to the show.
Yesterday the ensuing row saw tensions surrounding the independence debate bleed into the Games. Within hours the Scottish Government was forced to deny that it had made the request.
A source close to First Minister Alex Salmond said it was "absolutely, categorically, 100 per cent" the case Scottish ministers had made no such demand.
For its part, the Ministry of Defence (MoD) highlighted the role of the Red Arrows as "ambassadors for the United Kingdom", insisting the use of red, white and blue had been appropriate. The official press programme for the event described how the Red Arrows would "fly overhead in a V-formation trailing blue and white smoke".
The proposal to use the Saltire colours is understood to have been the brainchild of a marketing firm hired by Games chiefs to work on the opening ceremony.
The Glasgow 2014 organisers yesterday said that the idea had been discussed with the Red Arrows, but that no formal request for a blue-and-white fly past had ever been made.
"Glasgow 2014 would like to clarify that it was its ceremonies' producers who had conversations about Red Arrows trailing blue and white smoke to represent the host nation's Saltire," a spokesman said. "But this was never formally requested."
A spokesman for the Red Arrows said that the display team itself did not have the authority to change its traditional colours. He added, however: "We flew with red, white and blue because that is what we always do."
The MoD declined to comment on reports the recently appointed Conservative Defence Secretary Michael Fallon, who was born in Scotland and educated at St Andrews University, had intervened to ensure that the red, white and blue smoke was used.
A spokesman for the MoD said: "The flypast was to celebrate the Glasgow Commonwealth Games, the Commonwealth and the presence of Her Majesty so it was fitting that red, white and blue were used."