Patrick Harvie cited a lack of engagement between the parties yesterday, 16 days after he shared a stage with First Minister Alex Salmond at the pro-independence campaign's launch in Edinburgh.
Green members will now be given the chance at their annual conference in October to decide if they want formal links with Yes Scotland.
Mr Harvie, co-leader of the party, said: "If we are to formally sign up as a party we need to know on what terms. We don't want to end up simply cheerleading for the SNP. It's entirely possible the membership takes the view that Greens help shape another pro-independence referendum campaign.
"Independence is a chance to change Scotland for the better, not stick with business as usual."
Tory leader Ruth Davidson said the campaign was "already falling apart" and an "utter shambles". "It is clear the cross party support Alex Salmond claimed for his separatist movement was nothing more than window dressing," she said.
"Alex Salmond's vast ego cannot even accommodate fellow Nationalists who want to break Scotland away from the United Kingdom."
Labour MSP Patricia Ferguson said the Yes campaign was in chaos. She said: "Things have gone from bad to worse.
"It looks like Patrick Harvie shares an experience many in the SNP have found – it is Alex Salmond's way or the highway."
Mr Harvie had hoped to recommend Yes Scotland to the 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.
A Yes Scotland spokesman claimed a "representative structure" for the campaign was currently being formed. He said: "Yes Scotland has been working well with Greens and we welcome the Scottish Green Party deciding their formal role at their annual conference.
"Many individual Greens are already making a real contribution to Yes Scotland and we look forward to the Green Party conference deciding to work formally within Yes Scotland or in parallel towards a Yes vote."
The campaign has been dogged by criticism with its glitzy launch, attended by actors Brian Cox and Alan Cumming, receiving a mixed reception and organisers having to revise the number of people who had signed the declaration after it wrongly claimed Twitter followers as supporters.
The Yes campaigners, who already have a £2million war chest, have called on the pro-union lobby to follow its lead and refuse large donations from outside Scotland.
The No campaign will label their bid to keep Scotland in the UK "Better Together".