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A Transport for London spokesman said: "The High Court has found that we were right not to run the Core Issues Trust's advertisement as it would have breached Section 149 of the Equality Act 2010.
"The advertisement clearly breached our advertising policy as it contained a controversial message and was likely to cause widespread offence to the public.
"This was borne out by the hugely negative public reaction the advertisement generated, including on social media and newspaper websites.
"We are taking steps to address the judge's comments regarding our internal processes."
The Christian Legal Centre (CLC), which is supporting Core Issues, welcomed the judge's criticism of TfL's "unfair" procedures.
Ben Summerskill, the chief executive of gay rights group Stonewall said:
Transport for London had refused to carry the ad on the grounds that it was "likely to cause widespread or serious offence to members of the public", and it contained "images or messages which relate to matters of public controversy and sensitivity".
Today the judge backed the TfL stance, despite her finding that there had been unfairness in its procedures.
The judge said TfL had applied its advertising policy "inconsistently and partially", but its refusal to display the gay ad was "justified and proportionate, in furtherance of the legitimate aim of protecting the rights of others".
The judge did, however, give permission for the Core Issues Trust to appeal to the Court of Appeal.
Although she did not think such an appeal would succeed, she said there were "compelling reasons" to allow it to go ahead.
She said the case "concerns interference with the right to freedom of expression which is a matter of such fundamental importance that it merits consideration by the appellant court."
The Mayor of London had decided to ban a controversial "gay cure" bus advert by a Christian group.
The ad read: "Not gay! Ex-gay, post-gay and proud. Get over it!" and Boris Johnson condemned it as "offensive to gays".
The Core Issues Trust Christian charity claimed that Boris Johnson was "politically driven" when he intervened to block the ad, but today a judge ruled that he did not abuse his position as chairman of Transport for London (TfL) when he imposed the ban.
Mrs Justice Lang, sitting at London's High Court, ruled that TfL's process in introducing the ban "was procedurally unfair, in breach of its own procedures and demonstrated a failure to consider the relevant issues".
But that was outweighed by factors against allowing the ad, including that it would "cause grave offence" to those who were gay and was perceived as homophobic, "thus increasing the risk of prejudice and homophobic attacks", said the judge.
The Mayor of London's decision to ban a Christian group's controversial bus advert about gay people was not unlawful, the High Court ruled today.