The billionaire businessman said he had listened to concerns about an announcement last week that the operator would no longer sell the newspaper on board its services.
The company had said the Mail, one of a handful of publications Virgin sold in its on-board shops, was “not compatible” with its “brand and beliefs”. It cited the newspaper’s stance on issues including immigration, LGBT rights and unemployment, which the firm said had caused "considerable concern" among train staff.
The tabloid called the move “disgraceful”, an attack on freedom of speech, and suggested its pro-Brexit stance may have influenced the decision. Mr Branson is an outspoken opponent of the UK’s departure from the European Union.
However, the Virgin founder denied the decision to pull the title from sale was “part of some grand campaign or at my behest” and said he and business partner Brian Souter had been unaware of the move until they read about it in the media.
Writing on the company’s website, he said they had “instructed our team at Virgin Trains to reconsider this decision and re-stock the Daily Mail”.
He wrote: “The decision was made in response to feedback from some of our Virgin Trains employees. Brian and I respect our people when they make decisions and we listen to their views. It is the way we have always run our companies.
“But we must also listen to the concerns voiced widely this week – by those who agree with The Mail’s editorial stance and those who vehemently disagree with it – that this move has been seen as censorship.
“Freedom of speech, freedom of choice and tolerance for differing views are the core principles of any free and open society. While Virgin Trains has always said that their passengers are free to read whatever newspaper they choose on board West Coast trains, it is clear that on this occasion the decision to no longer sell The Mail has not been seen to live up to these principles.”
Mr Branson added: "Brian and I agree that we must not ever be seen to be censoring what our customers read and influencing their freedom of choice. Nor must we be seen to be moralising on behalf of others."
He said the Virgin Trains would "undertake a full review of their sales policy, making clear that this policy should not single out individual media titles".