A spokesperson for the government department for Digital, Culture, Media and Sport (DCMS) says that it disagrees with the European Commission's stance and is "deeply disappointed that it has waited until after United Kingdom cities have submitted their final bids before communicating this new position to us".
The UK had been scheduled be the host in 2023, with several cities including Leeds, Dundee and Belfast already preparing bids.
A week before the shortlist for the 2023 award was to be announced, the European Commission ruled that United Kingdom involvement "will not be possible", adding that it was "one of the many concrete consequences" of Brexit.
She has also written to Martine Reicherts, director general for education, youth sport and culture at the European Commission, urging her to reconsider the decision not to allow Dundee to participate.
A DCMS spokeswoman said that while the United Kingdom would be leaving the European Union, it was not leaving "Europe".
Cities from non-EU countries have previously held the title but it must be a candidate to join or must be in the European Free Trade Association or the European Economic Area.
IT is right that there should be a proper investigation into our apparently-failed European Capital of Culture bid.
Dundee's chances of winning the title were effectively wiped out with the stroke of a pen, just days before a delegation was due to head to London to pitch their bid to be named the UK's entry.
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The European Commission also said that the United Kingdom will not be allowed to host the event in future years.
British politicians tore into the European Union over the decisions branding it "bitter" and hugely "disrespectful" to the cities who could have been told after the referendum 18 months ago.
"As is usual with cultural programmes and competitions, the United Kingdom government bears no responsibility for the financial investment made by the cities and councils", the department said.
"The European Commission must now explain why it has chose to engage in blatant discrimination against the bid from Leeds".
"We disagree with the decision and we are particularly disappointed that we've been informed of this after the cities submitted their bids", a spokesperson for Prime Minister Theresa May said.
"We want to continue working with our friends in Europe to promote the long-term economic development of our continent, which may include participating in cultural programmes".
"Some cities have already spent up to £500,000 on their bid submissions".
The only two previous British cities were Glasgow in 1990 and Liverpool in 2008.
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