The elections watchdog said the only process it would get involved in was the one being initiated by the Scottish Government, which will ask it to judge the appropriateness of Holyrood's proposed question or questions.
Last night, the SNP said pro-UK parties had been humiliated after the commission had "thrown out their attempts to hijack the referendum process".
However, Scottish Labour said it was pleased the Commission's system of assessing questions would involve neutral experts, not just party politicians.
Earlier this week, Scottish Labour, Conservatives and Liberal Democrats announced the creation of a three-person panel to look at the crucial question to be asked in 2014.
They enrolled Lord Sutherland of Houndwood, who in 1997 chaired the commission into long-term care for the elderly, Professor Matt Qvortrup, a constitutional expert, and Ron Gould, Canada's former assistant chief electoral officer, who wrote the critical report into the 2007 Scottish parliamentary elections.
Scottish Labour explained the panel would work independently of the pro-UK parties and the question they produced would "then be submitted to the Electoral Commission for rigorous scrutiny to ensure it is simple, clear and neutral".
However, John McCormick, the Electoral Commissioner, said: "It's for the relevant government to propose a question. It 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."
Last night, Angus Robertson, the SNP's campaigns director, 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 it is for the Scottish Government to propose the question and the Scottish Parliament to approve it, which is exactly what is happening."
However, a spokesman for Scottish Labour said it was pleased the watchdog had made clear experts would have a key role in its assessment.
He added: "The debate is not about who sends what letter to the Electoral Commission but about who frames the question – politicians or neutral experts.
"The SNP wants to choose the question itself; everybody else is urging independent experts to frame it."
The spokesman insisted the three-man panel would bring a real impartiality and neutrality to framing the question.
He said: "It is not too late for the SNP to work with the experts, not against them.
"Angus Robertson's extraordinary claims the commission supports the SNP's views on where the legal power lies will fool no-one."