The Sunday Herald revealed last week that after months of consultation meetings, the regional council of GMB Scotland, which has 56,000 members, had decided the union would campaign for a No vote and better devolution in the UK.
The move was hailed by the Better Together campaign, but denounced by some GMB members.
Jim Moody, an SNP member and GMB steward at Scottish Borders Council, said members were "incandescent" at a "disgraceful stitch-up".
Some GMB consultation meetings had single-figure audiences, undermining the exercise's credibility.
Now the Sunday Herald has learned that in early 2013, months before its consultation exercise had finished, GMB Scotland worked with the Labour Party to found United with Labour, the Labour-only No campaign for those unwilling to work with the Tories in Better Together.
The work was reported by Harry Donaldson, GMB Scotland's general secretary, in a largely unnoticed speech to the GMB conference in June. Donaldson told delegates Labour's involvement with Better Together was "an own goal", a feeling GMB Scotland "made known to the party".
He explained: "To join with the Tories would be to betray all that we stand for and have campaigned against in this union of ours".
He then revealed GMB Scotland lobbied Labour for a separate message "setting out a vision of a Scotland within the United Kingdom", adding: "I am happy to report to congress that the Labour Party have at last listened and have now launched United with Labour."
In the same speech, Donaldson also warned independence could wreck the UK Labour Party.
"Do not underestimate the significance of this referendum on the rest of the UK and our ability to return a Labour government to power.
"If Scotland became independent … there would be a loss of 40 Labour MPs at Westminster, a major blow for … achieving the return of a Labour government."
He attacked those on the left who saw independence as a way of delivering socialism as "at best naïve, and at worst delusional".
Under referendum legislation, each union can spend up to £150,000 promoting its position in the final stage of the campaign.
Unions representing more than 100,000 Scots workers have so far backed a No vote, without balloting their members, and before the SNP Government has published its White Paper on the mechanics of independence.
In addition to the GMB, the shopworkers' union Usdaw, rail union Aslef and the Community union, which together have 50,000 Scots members, have backed a No vote after UK-wide delegate meetings.
Public-sector union Unison, the white collar PCS, postal union CWU, and building union Ucatt, which together have more than 200,000 Scots members, are still consulting on what to do in the lead-up to the referendum, although none is directly balloting members.
Unite, which has 150,000 Scots members, and the teachers' and lecturers' union EIS, which has 56,000, are taking no position.
Unions argue they have always used collective decision-making and it is too costly to ballot members on each issue, including independence.
"What's the point in us doing a referendum of our members when they get to vote in the real referendum?" said one senior official.
But Chris Stephens, secretary of the SNP Trade Union Group, said the magnitude of September 2014 justified a change in approach.
A Unison member for over 20 years, he said: "If unions take a position without an open and transparent process they face a backlash from both sides."
Donaldson denied there had been a "stitch-up" for a No vote, and said he never gave a steer to members in the consultation, despite the behind-the-scenes work on United with Labour.
He said: "Until the outcome of the consultation we were not committed either way. We were not pushing a certain line, we were just inviting people to give their views.
"Most people would not have been at congress and would not have heard that speech. I never repeated that speech at any of those meetings.
"We are very comfortable with the process we went through."