Brian Wilson said Nationalists were importing loaded political language from Ireland, which risked inflaming tension between Catholics and Protestants in Scotland.
He said lumping the pro-UK parties together as “Unionist” was part of a knowing effort to link supporters of the United Kingdom with Ulster Unionism and “the Orange vote”.
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He said: “By putting that tag on, and in the full knowledge of that connotation in an Irish context, they know exactly what they’re doing. It’s a very dangerous road they’re going down.”
The remarks were recorded at a fringe event at last month’s Scottish Labour conference.
He denied his use of the word “Nationalists” was the other side of the same coin.
A recent government-commissioned report warned church and community leaders also feared a “subtle form of sectarianism” had now entered the constitutional debate.
Mr Wilson said when Nationalists grouped supporters of the UK together as “Unionists” it “obviously mirror images Ireland, where the political divide is also about the constitution”.
He said: “One of the worrying things I see going on here is... a very deliberate attempt being made to sectarianise Scottish politics. That is very dangerous.
“The word Unionist in Scottish politics is not a Scottish word. It is not Scottish Unionism.
“When Tory candidates stood [in the past] as Conservative and Unionist candidates in Scotland they were not talking about Scotland, they were talking about Ireland, and they were playing for the Orange vote in Scottish politics.
“That is the Unionist, that is Unionism, in Scottish politics.
“So when the Nationalists, when the whole thrust is to lump us together as Unionists... by putting that tag on, and in the full knowledge of that connotation in an Irish context, they know exactly what they are doing. And it’s a very dangerous road they’re going down.
“It’s a difficult thing to analyse, a difficult thing perhaps to see it happening. But it’s been happening over a long period and I think it’s really sinister.”
Although often sidestepped by politicians, religion is a recognised factor in Scottish politics.
In recent years, Catholic voters have largely swung away from Labour to the SNP, to the point where they were the most pro-Yes religious group in the last independence referendum.
Meanwhile, the largest pro-UK event of 2014 was a march organised by the Orange Order.
The historian Professor Sir Tom Devine has also written about how Mr Salmond, while SNP leader, courted Catholic voters who had previously seen the party as quasi-Protestant.
A YouGov poll for the Catholic journal The Tablet identified “a huge swing” by Catholic voters to the SNP in the 2015 general election had helped ensure Labour’s virtual wipe-out.
A Scottish Labour source confirmed many in the party were uneasy about the Unionist tag.
The source said: “A number of high profile Labour figures over the years have rejected the term Unionist because of its connotations with Irish politics, and many members feels the same way. Labour is a pro-UK party and our firm commitment to the United Kingdom and opposition to independence is based on the shared values of working people.”
Mr Wilson, 68, was an Ayrshire MP from 1987 to 2005, a minister in Tony Blair’s government from 1997 to 2003, and has been a non-executive director of Celtic plc since June 2005.
Pro-independence Green MSP Ross Greer said: “We’ve heard plenty of Labour figures describing themselves as ‘unionists’ over the years, so it’s surprising that Brian Wilson would object only when independence campaigners use the term.”
An SNP spokesman said: “Whatever our different opinions on independence, all parties should ensure that debate is conducted with courtesy, understanding and respect.
“Far from seeking division, we hope to unite everyone around the very simple principle that Scotland’s future must be Scotland’s choice.”