Private correspondence obtained by The Herald shows Mr Salmond's office has been helping campaigners wanting to widen the referendum to build the case for putting "devo max" to voters in the poll.
Evidence of the First Minister's active involvement in moves for second question last night angered political opponents and will dismay many within the SNP, who favour a straightforward Yes/No vote on leaving the UK.
Patricia Ferguson, Scottish Labour's constitutional spokeswoman, said: "We have suspected for some time that Alex Salmond wants a fall-back option on the ballot paper and this proves his advisers have been secretly colluding to help make this happen."
Publicly Mr Salmond has maintained his preference is for a single question on independence, while leaving the door open in case other options emerge. He has argued it would be his duty to include a second question if there is a groundswell of support.
However, an email obtained by The Herald shows the First Minister has been working behind the scenes to generate such support. The message was sent from Mr Salmond's special adviser Alex Bell to Martin Sime, chief executive of the Scottish Council for Voluntary Services (SCVO) and a leading proponent of a two-question poll.
The SCVO is the driving force behind the Future of Scotland group, a loose coalition of charities, churches, student organisations and trade unions which, since launching earlier this year, has been developing a possible second question on greater devolution.
Mr Bell's email, on June 14, provides a link to an internal report by the Unite trade union showing 62% of their members favoured a second question on devo max, according to a poll.
A message attached said simply: "Read this."
The SNP issued a press release on the Unite poll a few days later, with SNP MSP Linda Fabiani describing it as a "huge blow to the anti-independence campaign".
Referring to Unite's backing for Scots Labour leader Johann Lamont, Ms Fabiani added: "If Johann Lamont isn't even listening to her own supporters any more who exactly is she listening to?"
A few days after that the Future of Scotland group published its own Ipsos Mori poll suggesting 56% of Scots wanted a devo max option in the ballot.
Scottish Liberal Democrat leader Willie Rennie said: "Despite his public protestations, Alex Salmond is increasingly desperate to get a second question on the ballot paper. The fact his henchmen are manipulating independent organisations behind the scenes to achieve that second question shows just how desperate he is."
Scottish Conservative constitution spokesman David McLetchie said: "This shows how Alex Salmond has been trying to manipulate matters which will provide him with a get-out clause in light of the inevitable referendum defeat."
Details of the SNP Government's clandestine assistance emerged as the row over a possible second questions threatens to explode this week.
The SNP's Strategy Minister Bruce Crawford is due to meet Scotland Office Minister David Mundell today to discuss the issue and Westminster's Scottish Affairs committee is set to issue a report – expected to reject the idea of a second question – on Wednesday.
Yesterday, Mr Crawford said: "Unlike the anti-independence parties, we acknowledge the strong support within civic Scotland for a second question, as underlined by the poll of Unite members.
"And the more the Tory-led anti-independence campaign continues to offer nothing to Scotland, the more they will simply encourage people to vote Yes to an independent Scotland – with the gap between support for independence and the Union now down to just nine points, needing only a 4.5% swing to bridge."
The pro-UK parties are opposed to a second question but, as opinion polls continue to show a big majority against independence, SNP ministers have fought harder and harder to keep the option alive.