The Electoral Commission has said it will not examine any proposed referendum question drawn up on behalf of the pro-union parties.
Labour, the Tories and Lib Dems have asked an expert panel to compose a question which would be submitted to the commission for testing.
But the commission said only the "relevant government" could propose a question.
The SNP said the decision was a humiliation for the pro-union campaign.
The panel includes academics Dr Matt Qvortrup and Lord Sutherland, along with elections expert Ron Gould.
Lord Sutherland, who is to chair the panel, said at its launch on Tuesday that the referendum "requires a clear, understandable, and unbiased question. For this to be done and seen to be done, it is essential to seek the help of the Electoral Commission".
But in a statement released on Wednesday, Electoral Commissioner John McCormick said: "As we said in our consultation response it's for the relevant government to propose a question.
"This should be independently and transparently assessed before it is put to parliament for approval as part of a clear, statutory process.
"We would not expect to undertake any question assessment that was not part of this process."
He added: "The commission's process for assessing questions includes asking voters, experts, campaigners and politicians for their views".
SNP campaigns director Angus Robertson said: "This is an utter humiliation for the Tories and the rest of the anti-independence parties, whose ham-fisted attempts to hijack the referendum process have fallen flat at the first hurdle.
"The Electoral Commission has made clear that it is for the Scottish government to propose the question and the Scottish Parliament to approve it, which is exactly what is happening.
"The Tory-led cabal which Labour and the Lib Dems have signed up to will not hijack Scotland's referendum. It will be the people of Scotland who will decide Scotland's future and will not be fooled by this Tory-led campaign."
Scottish Labour said the debate was not about who sends a letter to the Commission but about who frames the question - politicians or neutral experts.
A spokesman said: "It is not too late for the SNP to work with the experts, not against them.
"Angus Robertson's extraordinary claims that the Electoral Commission supports the SNP's views on where the legal power lie will fool no-one."
The Scottish government wants to hold the referendum in autumn 2014.
The pro-independence SNP had said it wanted a straight yes or no question, but it was open minded on whether a second, so-called "devo max" question, on more devolved powers to Holyrood should be posed.
Nationalist leader and Scotland's First Minister Alex Salmond has already put on record that he intends to ask the country's electorate: "Do you agree that Scotland should be an independent country?"
He has also said that the Electoral Commission would test and scrutinise the final question.