It plans to publish a series of papers over the coming months that will look at Scotland's current position, and the choices it would be faced with if the country voted to leave the UK.
However, Michael Moore warned that this work would not open up negotiations, or "set out a contingency plan" for independence.
Westminster will this week debate legislation which will allow the Scottish Government to hold a "legal, fair and decisive referendum", as agreed by the two administrations last year in the Edinburgh Agreement.
Writing in a Sunday newspaper, Mr Moore said: "Many of the big issues are already being discussed: the effect independence would have on Scotland's economy; what armed forces would be affordable and desirable; and the uncertain terms on which an independent Scotland would seek to become a member of the EU, Nato and other international organisations.
"But we need the 'great debate' to flush out all the issues. Over the next few weeks and months the UK Government will start publishing a series of papers that look at Scotland's position in the UK today and make clear the choices that would face all of us as Scots if the UK family were to break up. This will be a serious body of work to inform the public debate.
"But what this work will not do is open up negotiations or set out a contingency plan for independence. The UK Government works for the whole of the UK including Scotland, and we are deeply committed to the United Kingdom.
"I and my Ministerial colleagues represent the whole of the UK; we cannot - and should not - negotiate or plan in the interests of only one part of it."
Mr Moore said that any pre-referendum negotiations would "start to unpick the fabric of the United Kingdom that is so fundamental to us all".
He said: "In any split, the hard decision to leave happens before the difficult work of dividing up assets and debts.
"I hope and believe that Scots will choose to keep the UK family together, not split it apart. But if I am wrong, and Scots vote to leave the United Kingdom, only then will negotiations between Scotland and the rest of the UK begin."
Meanwhile, First Minister Alex Salmond said the passing of legislation to allow a referendum would represent a move from a debate on process to one on substance.
Writing in another paper, Mr Salmond said 2013 would be the year the SNP would "spell out the huge opportunities" that would come with a yes vote.
He said: "There are many good reasons for an independent Scotland. We will explain how, by extending and completing the powers of the Scottish Parliament, we can deliver a better and fairer society for all the people of Scotland."
He added: "The referendum will ask one question, but in truth Scotland faces two choices - the first is whether to bring the powers home to govern ourselves, rather than sticking with Westminster.
"And the second is - what kind of society do we want to be?
"But we don't get to make the second choice without being prepared to make the first. The powers of independence are tools we need to build the country we want to be."
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