Scottish Government figures which show it spends nearly 10% more than it raises in taxes are relatively vague and do not provide the definitive position for Scotland, according to Economy Secretary Keith Brown.
Mr Brown met UK International Trade Secretary Liam Fox in Edinburgh to discuss measures to boost trade and construction to create "maximum prosperity, employment and stability" in Scotland.
Both ministers said the meeting was constructive despite disagreements over Brexit, which the Scottish Government says will damage the economy.
Read more: Economic deficit 'would not disqualify Scotland from EU membership'
The SNP is considering a range of options to keep Scotland in the EU, including a second independence referendum.
The meeting followed publication of the Government Revenue and Expenditure Scotland (GERS) figures showing Scotland's deficit has risen to £14.8 billion - or 9.5% of Scotland's gross domestic product.
Speaking after the meeting, Mr Brown said: "That deficit, of course, accrues in the current constitutional settlement. A different set of calculations are made, I believe, in relation to an independent Scotland.
"Some of the figures are relatively vague that come out from GERS that come from the UK Government.
"They don't take into account, for example, the disproportionate spend in Scotland for defence expenditure.
"So these figures are incomplete and I don't believe provide the necessary and definitive position for Scotland.
"Of course, it is the case that we didn't have a success in the referendum in 2014 in terms of us being independent, so these figures reflect the current constitutional position."
Earlier, Scottish Finance Secretary Derek Mackay said the deficit would not disqualify Scotland from EU membership. The EU stability and growth pact urges member states to keep deficits below 3%.
Read more: Economic deficit 'would not disqualify Scotland from EU membership'
Mr Brown said: "There are countries in the EU which have deficits in excess of 10%."
He added that the meeting with Mr Fox was "straight-talking and, in parts, constructive".
"I made clear, of course, the different approach that the Scottish Government has in relation to the impact of Brexit," he said.
"I also made clear that we expect the UK Government to support the measures taken by the First Minister in terms of accelerating capital projects to help the economy, and asked that that be brought forward in the UK Budget.
"And we agreed, I think, substantially on the need for Scotland to increase its trade activity, both in terms of promoting Scotland, its companies and its economy, and in working with the UK Government where that makes sense."
He also said it makes sense to work with the UK Government on international trade missions where they have shared objectives.
Mr Brown called for more leadership from the UK Government in developing a Brexit strategy.
"At the top level, in terms of the Treasury, the Chancellor and the Prime Minister, we're not seeing leadership.
"Many of these people wanted Brexit and it's really down to them to map out what they think should happen, and we're not seeing that.
Read more: Economic deficit 'would not disqualify Scotland from EU membership'
"To be fair to Liam Fox, he has some ideas in relation to trade, which are welcome, but we do need to see an overarching strategy for how the UK deals with the legacy of this unnecessary vote for Brexit."
Dr Fox said the meeting was "very constructive and very positive".
He added: "We want the same things, which is to see maximum prosperity and employment and stability in the Scottish economy."
Asked how he would protect Scottish exports after Brexit, he said: "We will be setting out our plans in detail for exports in the coming months."
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