The Pope made his remarks in his opening address to the Queen at Holyroodhouse in Edinburgh.
He said: "Even in our own lifetimes we can recall how Britain and her leaders stood against a Nazi tyranny that wished to eradicate God from society and denied our common humanity to many, especially the Jews, who were thought unfit to live.
"As we reflect on the sobering lessons of atheist extremism of the 20th century, let us never forget how the exclusion of God, religion and virtue from public life leads ultimately to a truncated vision of man and of society and thus a reductive vision of a person and his destiny."
A statement from the British Humanist Association said the Pope's remarks were "surreal".
It said: "The notion that it was the atheism of Nazis that led to their extremist and hateful views or that it somehow fuels intolerance in Britain today is a terrible libel against those who do not believe in God.
"The notion that it is non-religious people in the UK today who want to force their views on others, coming from a man whose organisation exerts itself internationally to impose its narrow and exclusive form of morality and undermine the human rights of women, children, gay people and many others, is surreal."
The rest at BBC News
A most excellent summary of the evidence for the Nazi/Christianity connection can be viewed here.
