The Scottish First Minister discussed how a vote could be staged when he met Michael Moore in Edinburgh this morning.
Afterwards, Mr Salmond said there were still two key issues of disagreement between his Scottish National Party (SNP) administration and Westminster.
These, he said, were whether or not the ballot should also give Scots the option of backing greatly-enhanced powers for Holyrood - dubbed devo-max - and whether 16 and 17-year-olds should be entitled to vote.
However, Mr Moore also identified the time of the referendum as an issue.
The Scottish Government has said it wants the vote to take place in the autumn of 2014 but Mr Moore said he still wanted it to be "sooner rather than later".
The talks between the two men had been scheduled to last about an hour but ended up going on for approximately 90 minutes.
Mr Salmond will also hold talks with Prime Minister David Cameron on the referendum on Thursday.
The First Minister said those discussions, and the talks with Mr Moore today, were being held "with a view to getting agreement on the manner in which the independence referendum will be held".
He added: "I think there was some modest progress this morning but I suspect the key points of disagreement have been identified as one or two questions, 16 and 17-year-olds voting."
The First Minister said he did not anticipate any agreement between Holyrood and Westminster on the issues until after the consultations that both governments are staging.
But he said it was "useful that it was clarified today that the Westminster Government were willing to listen to their consultation on these matters".
Mr Salmond said the Scottish Government had an "open mind" as to whether there should be a devo-max option on the ballot paper.
He also said they were "favourable to 16 and 17-year-olds getting the vote" before adding: "We will listen to the consultation exercise and I hope that once the consultation is completed and the process is completed then that will enable us to come to agreement, that will shift the ground."
The First Minister added: "Hopefully the voice of the people will prevail upon the politicians to find common ground on these matters and the objective is to have the referendum in the timescale that we indicated."
He stated: "You wouldn't have expected us to come out with complete agreement, it's modest progress."
Mr Salmond insisted there was not a "serious argument" between the two administrations on the timing of the referendum.
He said: "There are different views, of course, on the timescale that the Scottish Government has set out. I don't think that is a serious argument any more."
The First Minister said this matter, together with the issue of what role the Electoral Commission would play in the referendum, were "more or less settled".
However, he added: "That's not the case, quite clearly, on the question of one or two questions and the questions of the 16 and 17-year-olds franchise.
"But at least there was the indication that the consultation on these matters is important."
Mr Salmond said it was "useful" that Mr Moore had "declared" the UK Government was willing to listen to the consultation on these matters, with the First Minister stating: "I think in terms of getting a resolution, then perhaps the voice of the people will be very, very important."
The UK Government has repeatedly stated that Holyrood does not have the authority to stage a referendum on independence, as the constitution is reserved to Westminster.
As part of its consultation, the coalition Government proposes using a Section 30 order to temporarily extend the Scottish Parliament's powers to enable a ballot to be held.
Mr Salmond again said he had "no difficulty" with this but stated: "Our difficulty, as you know, was with the conditionality, with the strings that are attached."
He also said he would make the case to Mr Cameron that "the Section 30 should be offered without conditionality, without strings".
The First Minister also commented on reports that Mr Cameron was only meeting him as a matter of courtesy.
Mr Salmond quipped: "Courtesy visits are usually what prime ministers do to foreign heads of state - I don't know if that's what Downing Street meant to imply."
He added: "The Prime Minister makes the decisions, that much is obvious.
"Michael Moore is the Secretary of State for Scotland, he's appointed by the Prime Minister - that's not meant to be a snub or any disrespect, that's just a statement of fact.
"If you are negotiating, you negotiate with the person or people who make the decisions. That, again, is just a statement of fact."
Mr Moore said the timing remains unresolved and suggested the ballot could be held a year earlier than proposed by the Scottish Government.
"We still believe that it would be better to have this sooner rather than later," he said.
"We certainly want to explore as a starting point - we don't anticipate agreement on this quite yet - but as a starting point, looking at the technical aspects of how you could deliver the referendum sooner than the Scottish Government has set out."
He said he would not "trade dates" but added: "There's not a problem to bring this forward to some stage in 2013.
"The key point is the technical issues that are deemed to be in the way at the moment, which I don't think are insurmountable, and the broader debate as part of the consultation about what is best for people in Scotland. I think sooner rather than later is best."
Mr Moore said he took from the meeting that September 2014 is the preferred timescale for the Scottish Government.
He said there was positive discussion on legal process and the role of the Electoral Commission, but not on the timing, franchise and number of questions.
He said: "We had a good, thorough and constructive discussion around all of those issues, respecting the fact that both Governments are conducting consultation on all the issues to do with the referendum."
On the potential for multiple questions, he said: "We think there are some very serious issues about that, in broad terms, about the decisiveness of the question, if you have more than one, but also just technicalities about how one might interpret the result."
Scottish Liberal Democrat leader Willie Rennie previously raised concerns that a slender majority for independence might trump a landslide majority vote for more devolution in a multi-option referendum.
On the potential for an extra question, Mr Moore said he would "look carefully" at the consultation responses.
But he added: "My strong view is that a single question is the way which would deliver a decisive outcome.
"The issue at stake for us here is determining Scotland's continuing place in the United Kingdom.
"I very thoroughly want it to continue to be in the UK. I am convinced that when we make a decision as a country, that is what we will decide.
"We think there are all sorts of technical issues around having more than one question that haven't even been begun to be addressed."
Mr Moore added that it is "entirely right" that the First Minister and Prime Minister should meet, but said his own position is "clear".
"On this central issue of the referendum, the Prime Minister is clear that he wishes me to get on and work this through with the First Minister," he said.
"This morning was a constructive first point on that journey."
Scottish Labour leader Johann Lamont said: "It doesn't bode well for Scotland's referendum that the First Minister and the Scottish Secretary can't even agree what they agreed at their meeting.
"It is becoming increasingly clear the SNP are determined to drag out the debate about process as a smokescreen for their faltering case for separation.
"If we are continuing to debate the timetable, the franchise and the wording of the question, then we are not talking about the things that matter to people.
"With big question marks about what currency we will have, how we will defend ourselves and whether there will be more or less jobs in an independent Scotland, the only person this distraction suits is Alex Salmond."
PA
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