Green co-convener Patrick Harvie, who stood alongside Alex Salmond at the launch of Yes Scotland just a fortnight ago in the expectation the Greens would join the campaign, said his party had formally decided not to join because the campaign had failed to include others in its decisions.
Harvie said he was "disappointed" at the lack of engagement with Yes Scotland, which is dominated by SNP money and personnel.
The Glasgow MSP said: "We can't just be there to wave the flag for someone else's campaign. We're either involved in shaping it or we're not.
"We feel frustrated by the lack of progress towards a genuinely inclusive campaign, and concerned that a non-inclusive campaign will be less likely to succeed." The decision not to join the campaign for a Yes vote in the 2014 referendum was taken by the Greens' ruling council last week.
It leaves the SNP and Scottish Socialists as the only political groups in Yes Scotland, undermining its claim to be a "big tent" movement capable of converting swing voters to independence. Unionist parties said the Greens' decision showed the limited appeal of the SNP's key policy, and claimed Yes Scotland was "an utter shambles".
The Greens will revisit their decision at their autumn conference in October, when they will discuss whether to join Yes Scotland, or whether to campaign for independence with another group.
Harvie said he had hoped to recommend Yes Scotland to his party council last week, but was unable to do so because the campaign had no firm plans for involving others in how it was run.
He said Salmond had floated some ideas about the Greens and SNP working together, but "none of them seemed to be concrete", leaving the Greens feeling shut out of the process.
"We have been knocking on the door and the door has not been opened," Harvie said. "If Yes Scotland is going to be a broad and inclusive campaign, as it needs to be, it needs to implement shared decision-making about the direction of the campaign.
"I hope that's what happens, and I would be keen to take a recommendation [to October conference] that we participate on those terms. But if those are not the terms then we will have to find other ways of campaigning for a Yes vote."
He stressed the differences with Yes Scotland were not over policy, but organisation.
He also said Green party members were free to help Yes Scotland on an individual level, while the party withheld its stamp of approval.
Although Yes Scotland has promoted itself as a campaign for those in all parties and none, behind the scenes it remains dominated by the SNP.
Its key personnel include two of Salmond's former political advisers, Jennifer Dempsie and Stephen Noon, and the SNP's election guru Angus Robertson, leader of the party's MPs at Westminster.
The campaign's £2 million war-chest also comes from donations given to the SNP, while Yes Scotland Ltd, the legal entity behind the campaign, has only one director, an SNP lawyer.
With no board or chief executive, this leaves SNP personnel in day-to-day control by default.
WHEN Yes Scotland launched, critics saw the lack of a board or boss as a sign of a rushed start. But it now looks more like a deliberate ploy to let the SNP keep sole control of the decisions on tactics, messages and spending.
Harvie said: "I can understand why, if you're putting in £2m, you would want to have some control. But if that's the approach they will have trouble because Yes Scotland needs to go beyond parties if it's to have a hope of succeeding."
It is understood the Scottish Socialists are also becoming unhappy with a lack of engagement with SNP players inside Yes Scotland, and at pro-independence events and marches being organised exclusively by SNP activists.
Scottish Conservative leader Ruth Davidson said: "Not even a fortnight in and the Yes Scotland campaign is already falling apart. It's clear that the cross-party support claimed for [Salmond's] separatist movement was nothing more than window dressing. This is an utter shambles."
Labour MSP Patricia Ferguson added: "It looks like Patrick Harvie shares an experience many in the SNP have found – it is Alex Salmond's way or the high way. "
SNP campaign manager Angus Robertson said: "We in the SNP have been working well with the Greens and others as the Yes Scotland campaign gears up.
"This will be progressing in the weeks and months ahead as we go from strength to strength."