As part of a major restoration project, workers will return decorative elements around the clock face of the Elizabeth Tower to their original Victorian colour scheme, including a row of shields bearing the red and white cross on the English flag.
Palace authorities said the other nations of the UK are represented in floral emblems elsewhere on the clock face, depicting the rose, thistle, shamrock and leek. However, SNP MPs said the decision was "odd" and "a welcome boost for Scottish independence".
Research into Charles Barry's designs, as well as analysis of samples taken from layers of old paint, confirmed which colours had been used when Big Ben was originally built in 1859.
Adam Watrobski, Westminster's principal architect said: “As part of the major repair and conservation of the Elizabeth Tower, we have carried out extensive research into the original decorative scheme for the clock faces and the adjacent areas.
"Using historic paint analysis and references including Barry’s original design watercolour, contemporary illustrations and archival photographs, we have recreated the original colour scheme.
"The dials and clock hands are Prussian blue and gold and the adjacent areas make use of the red, white and blue colours of the Union flag, along with the detail colours used for heraldic shields for each part of the United Kingdom.
"The existing gilded areas closely match those that were gilded and these have not changed significantly during the life of the Tower. This will very much be the crowning glory of this important project and will certainly serve to reinforce the symbolism of the Tower in its international representation of the United Kingdom.”
Tom Brake, the Liberal Democrat MP who chairs the House of Commons commission, said the restored design "represents what is best about England and the English nature".
He added: “Obviously the Scots, the Welsh and Northern Irish are represented on the tower with the different rosettes that are there representing those countries, so I’m sure they won’t object to that.”
But SNP MP Tommy Sheppard said: "Maybe they are assuming that in the future the Union will be dissolved.
"It seems very odd. I think you would have the Union Flag or all the flags for the component parts of the UK.
"It certainly makes a statement if they are only using the St George's flag. I don't think they have thought through the political consequences."
His SNP colleague Pete Wishart added: "This is a welcome boost for Scottish independence as Westminster prepares to become an England-only parliament.
"People will, however, be forgiven for thinking that transition began long ago - as Scotland continues to be sidelined and ignored on the biggest issues facing our country.
"Whether Scotland opposes Brexit, austerity, Trident, or the devolution power grab, our views never seem to matter to a Tory government that arrogantly thinks it can do whatever it likes to Scotland and get away with it."
Big Ben has been under scaffolding since last year, when four years of work to restore the clock tower began. A Â£4bn restoration programme for the rest of the Palace of Westminster has been agreed by parliamentarians but is not set to start until the 2020s.