In a lengthy "historical note" at the end of his new novel, Dominion, he says beneath the "empty populist bonhomie of Alex Salmond, the prospective break-up of Britain is already creating a new culture of hostility and bitterness on both sides of the Border."
Sansom, from Edinburgh, adds: "A party which is often referred to by its members, as the SNP is, as the National Movement should send a chill down the spine of anyone who remembers what those words have often meant in Europe."
The author, known for his successful series of historical crime thrillers featuring lawyer Matthew Shardlake, had a best-seller with his last stand-alone novel, Winter in Madrid.
Dominion, to be published on October 25 by Mantle, takes place in an alternative future where the UK has surrendered to the Nazis after Dunkirk.
Sansom sold more than half-a-million copies of Winter in Madrid, with total sales for his books standing at around three million.
He says in his notes: "I find it heartbreaking – literally heartbreaking – that my own country, Britain, which was less prone to domestic nationalist extremism between the wars than most, is increasingly falling victim to the ideologies of nationalist parties."
He adds: "It does not take more than a casual glance at its history to show that the SNP have never had any interest in the practical consequences of independence.
"They care about the ideal of the nation, not the people who live in it."
In a further email, the author told The Herald he thinks the SNP are "deeply dangerous" and added: "Like all nationalist parties the SNP define themselves against a hostile 'other,' which in the case of the SNP has always been England, although when Salmond's mask of bonhomie slips, as it often does, he talks of Scotland being unfairly treated by 'the UK'.
"The SNP like to present themselves representing a new type of politics, but nationalist populism is actually a very old and mangy European beast.
"It promises everything to everyone, but the SNP is an empty shell when it comes to detailed policies and where the money to pay for them is to come from.
"Where they do have policies they are often contradictory."
He added: "Their attempts to gerrymander the referendum in their favour by lowering the voting age and holding it around the anniversary of Bannockburn should make any Scot wonder what sort of party they will be putting in power in their newly independent state, perhaps forever.
"Finally, I think it is a shame that much of the debate has been couched in terms of 'Scottish patriotism' versus 'UK patriotism'.
"I fear the rise of parties based on national identity politics on both sides of the Border and all across Europe, given the Continent's history over the last century, and this is the point I want to put into the debate."
In his notes, he writes: "If this book can persuade even one person of the dangers of nationalist politics in Scotland and in the rest of Europe ... it will have made the whole labour worthwhile."
Born in 1952, Christopher John Sansom grew up in Edinburgh, the only child of an English father and a Scottish mother, Trevor and Ann, to whom Dominion is dedicated.
He has described his family upbringing as "traditional Presbyterian" and he studied history at Birmingham University, after which he studied law and practised in England in the legal profession before becoming a writer.
He added: "The point I am trying to make in Dominion is that parties which believe only in national identity politics and nothing else can go down dangerous paths, with dangerous bedfellows."
James Robertson, the Scottish author, who often confronts issues of Scottish identity and politics, said: "Christopher Sansom seems to be singling out the SNP as particularly dangerous, whereas their history shows them to be one of the mildest-mannered of 'national movements' that ever existed.
"The SNP are avowedly and demonstrably non-racist, and as socially inclusive and progressive as, say, Labour or the Liberal Democrats.
"The notion that a Yes vote in the independence referendum will usher in an era of one-party rule, 'perhaps forever', is particularly far-fetched."
An SNP spokesman said: "Sadly, CJ Sansom knows nothing about the SNP or the positive case for independence which embraces Scotland in all of its diversity – he would be more than welcome to visit SNP conference next week to do some basic research before any future writings."