Nicola Sturgeon has written to Deputy Prime Minister Nick Clegg, calling for such an approach to enable "sensible preparations" to be made in the event of a Yes vote.
Scottish Secretary Michael Moore has insisted that the UK Government will not enter negotiations over the terms of Scottish independence before the referendum.
But in a new blog on the Scottish Government's referendum website, Ms Sturgeon said: "I disagree strongly with Michael Moore's statement at the weekend that there should be no pre-referendum discussions between our two governments."
She said she hopes "common sense will prevail", writing: "Before Christmas, I wrote to Nick Clegg, who is responsible for constitutional matters in the UK Government, to suggest this common sense approach - open exchange of information and sensible preparations for a Yes vote."
The Deputy First Minister, who has responsibility for constitutional matters, said all parts of the Scottish Government would be "working on a transition plan considering what needs to be done to give effect to the decision of the Scottish people when they vote Yes, as I believe they will".
This work would encompass the "administrative steps that will require to be taken, the legislation that will require to be passed, the matters that will require to be negotiated with the UK government", she said.
"This transition work should also be discussed, on an ongoing basis, with the UK government in order that we develop a shared understanding of what these issues are and, as far as we can, a shared approach to dealing with them.
"After all, on many issues, currency for example, our interests will align - what is in Scotland's best interests will also be best for the UK."
Ms Sturgeon is "not suggesting that we should 'pre-negotiate' the independence settlement" but "I am saying, very clearly, that we must do the groundwork now to ensure that, in the event of a Yes vote, both governments are in a position to work together constructively in the best interests of the people of Scotland and the rest of the United Kingdom."
It is "clearly in the interests of both Scotland and the rest of the UK that such discussions do take place".
She said: "I would have thought that the Secretary of State for Scotland, of all people, would see the sense in that. After all, even though he opposes independence, he will surely want the best deal for Scotland in the event that we do vote Yes."
After the SNP deputy leader previously said that unionist politicians would be invited to any negotiations for Scotland to leave the UK if the vote is for independence, she suggested that Mr Moore "may well have a part to play on Scotland's behalf".
While the UK Government plans to publish a series of papers examining Scotland's current position and the choices it would be faced with if it voted to leave the UK, Mr Moore said this would not "set out a contingency plan" for independence.
In an article on Sunday, Mr Moore said: "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."
Any pre-referendum negotiations would "start to unpick the fabric of the United Kingdom that is so fundamental to us all", Mr Moore argued.
"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."
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