The newspaper has accused Virgin of censorship in response to the move.
The train operator said it made the decision in November, pointing out in an internal note to staff that “considerable concern” had been raised by colleagues about the newspaper’s editorial position on issues such as immigration, LGBT rights and unemployment.
But the newspaper said Virgin Trains told them the only reason the paper would no longer be sold was to “save space”.
A spokesman for the Daily Mail said: “It is disgraceful that, at a time of massive customer dissatisfaction over ever-increasing rail fares and after the taxpayer was forced to bail out Virgin’s East Coast mainline franchise, a decision strongly criticised by the Mail, that Virgin Trains should now announce that for political reasons it is censoring the choice of newspapers it offers to passengers.
“It is equally rich that Virgin chose to launch this attack on free speech in the Aslef trade union journal.
“For the record, Virgin used to sell only 70 Daily Mails a day.
“They informed us last November that to save space, they were restricting sales to just three newspapers; the Mirror, FT and Times.
“They gave no other reason, but it may be no coincidence that all those titles, like Virgin owner Sir Richard Branson, are pro-Remain.”
A spokesman for Virgin Trains said: “We regularly review the products we have on sale for customers in the shop on board our West Coast trains and after listening to feedback from our people, we decided in November 2017 that we would no longer stock copies of the Daily Mail.
“When we stocked the Daily Mail onboard, we sold one copy for every four trains.”
In an internal note to staff within its West Coast business, Virgin Trains wrote: “Different viewpoints are often valuable and it’s certainly true that we choose to take our news from different sources depending on our view of the world.
“Thousands of people choose to read The Daily Mail every day.
“But, from Sunday 26 November, they will no longer be reading it courtesy of VT.
“There’s been considerable concern raised by colleagues about The Daily Mail’s editorial position on issues such as immigration, LGBT rights and unemployment.
“After due consideration, we’ve decided that this particular paper is not at all compatible with the VT brand and our beliefs.
“We will continue to offer The Times to customers, but we won’t be stocking the Daily Mail for sale or as a giveaway.
“This won’t suit all of our customers or all of our people, it’s certain to draw some criticism.
“But we’ve listened to many colleagues over the last few months, and we feel that this is the right move to take. #vtnews”
Ian Murray, executive director of the Society of Editors, said: “We are very concerned about this move.
“It smacks of censorship and, regardless of whatever publication is being targeted, this is the start of a very dangerous slippery slope.
“Although Virgin Trains has every right to decide what products it wishes to sell, it’s clear that there are motives of censorship behind their decision, which is to be deplored.”