The word Christmas in one of his snowy DVD’s has been replaced with “the winter holiday”.
And even Christmas trees get the chop as they are renamed “trees with decorations”.
The DVD called Little Engine’s Big Days Out tells the story of how Thomas and his engine friends escape the snow.
It is narrated by Michael Angelis who tells little viewers: “You’ll always see a tree with decorations during the winter holidays.”
Church leaders and campaigners have now accused Hit Entertainment, owners of Thomas, of being politically correct.
John Midgley, co-founder of the Campaign Against Political Correctness, said: “This is another example of the attempt to write Christmas out of something which is so popular with families.
“Let’s hope the makers of the DVD think hard about this. It’s out experience that people from other religions do not want to eradicate Christmas from holidays or write it out of our everyday language.
“We feel it is vital not to do this especially when the audience is children.”
A spokesman for the Catholic Church said: “It would be a great shame if political correctness were to wipe out the true meaning of Christmas for children, even to the extent of interfering in classic children’s stories.
“It is ironic that this series is affected, especially as the original author was a Christian minister.”
And the Rev Mark Johnstone, convenor of the Mission and Discipleship Council of the Church of Scotland, said: “There is a great Christian tradition in Scotland and Christmas is important as it celebrates the birth of Christ.”
Multi-million pound Thomas was created by Christian clergyman the Rev Wilbert Awdry.
Thomas was intended as a Christmas present for his son Christopher.
But today he is the star of DVDs and is sold in supermarkets and toy shops throughout the world.
A spokeswoman for Hit Entertainment said: “The DVD is not a seasonal release and thus its content spanned more than just Christmas.
“When we do have seasonal specific releases, our focus is very much on the particular event being celebrated.”
She added that the company had previously released a Christmas Express and will follow this up with a Merry Christmas Thomas.
Other attempts to write off Christmas have included Dundee Council replacing it with “Winter Light Night” in 2009.
The Red Cross charity shops have also banned nativity scenes from their window displays at Christmas.
And Inland Revenue staff were banned from donating to a charity which helps send toys to needy children because of its links to Christianity.