In a significant hardening of the Coalition's position, Mr Moore said if there was a second question on the ballot paper "I don't think we can have a referendum on independence".
His comments – the strongest yet on the so-called devo max option – come ahead of crunch meetings tomorrow between the UK and Scottish Governments.
First Minister Alex Salmond and Prime Minister David Cameron will come face to face for the first time in months during a meeting of the Joint Ministerial Committee in Downing Street, at which the topic of the referendum is expected to be discussed.
Mr Moore will also have his second meeting with Nicola Sturgeon after she took over responsibility for the referendum in the Scottish Government.
Mr Moore told members of the Commons Scottish Affairs Committee her appointment showed the two governments were keen to come to an agreement over the referendum.
He said he hoped they would reach that agreement by October 22 "with a fair wind".
He also revealed the two governments planned to publish a political statement of intent alongside the legal arrangements for the independence vote.
This would not be legally binding but would include the political intent of both governments, Mr Moore said.
However, he insisted the issue of how many questions would appear on the ballot paper would be included in the legal order allowing the Scottish Government to hold the referendum, and would be binding. He said there would only be one question put to voters.
"I don't think we can have a referendum on independence if we don't have a single question," he said.
"The expectation in Scotland is that we need to resolve this issue of independence."
He said there were a number of reasons for just one question, asserting that independence was very different from further devolution and there was no "sliding scale" between the two.
He also said that because no-one had defined it, "there isn't a second question to ask".
He added: "There isn't a body of opinion out there that has given us a fully formed question on the next stage of devolution beyond the Scotland Act."
He also warned that the outcome of any two-question ballot would be "difficult to interpret". He added: "No-one would have confidence in the outcome if you are arguing what is meant by the outcome."
Ian Davidson, the chairman of the Scottish Affairs Committee, also told Mr Moore he thought "anything other than a single-question referendum would not pass through this parliament, so that makes a difference".
Under the legislation, both Holyrood and the Commons have to agree to the Section 30 order, which would in effect lend the Scottish Parliament the legal power to hold a referendum on independence.
A spokesman for Deputy First Minister Nicola Sturgeon said: "This is Scotland's referendum, and the arrangements for it should be made in Scotland, not dictated by Westminster. All of the relevant issues governing the referendum, including that of a second question, must be determined in the interests of the Scottish people."
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