The Institute for Fiscal Studies (IFS) said the country's borrowing would amount to 3.6% of Gross Domestic Product (GDP) in 2017/18, the second full year of independence under Alex Salmond's timetable for leaving the UK.
By contrast, UK borrowing was estimated at 1.2% of GDP.
The figures are based on last December's oil and gas revenue forecasts from the UK's Independent Office for Budget Responsibility (OBR). They take into account improvements in the economy and the Chancellor's decision to extend his austerity programme.
The OBR expects the North Sea to produce £3.3 billion in tax revenues in 2016/17, down from a previous estimate of £4.5bn.
The latest IFS analysis, unveiled as the director of the think tank Paul Johnson addressed a seminar at Holyrood, highlighted the gulf between the OBR's oil and gas forecasts and the Scottish Government's own figures.
The SNP's independence White Paper estimates the North Sea will yield up to £7.9bn in 2016/17 - more than double the OBR figure.
Using the higher Scottish Government figure, an independent Scotland's borrowing would be 1% of GDP in 2017/18, a lower level than in the rest of the UK.
In its analysis, the think tank raised doubts about the reliability of the Scottish Government estimates, saying ministers had been too optimistic about oil revenues this year and last.
Overall, the IFS said the finances of both the UK and Scotland looked in slightly better shape in the medium term as a result of economic recovery and Chancellor George's Osborne's decision to extend his austerity programme for an extra year into 2018/19.
The report said: "This is good news but would require the government of a newly independent Scotland to continue with the spending squeeze planned by the coalition government. The latest OBR forecasts also illustrate the sensitivity of Scottish public finances to oil revenues. Neither the OBR nor the Scottish Government can know for sure what will happen to these revenues.
"Fiscal decisions in an independent Scotland would need to be taken in the context of considerable uncertainty over this important part of the budget - and in the context of long-term pressures both on these revenues and arising from an ageing population.
"The new forecasts do little to diminish the tough choices that will face Scotland (and, to a lesser extent, the UK) if it is to achieve long-run fiscal sustainability."
Scottish Labour's finance spokesman Iain Gray said: "The SNP's whole case for an independent Scotland's prosperity is predicated on oil revenues.
"The reality is that even though there may be plenty of oil left, the cost of recovery and the fluctuation in price means it's not credible to build the economy of a nation on one income stream that isn't stable or sustainable.
Scottish Conservative finance spokesman Gavin Brown MSP said: "The IFS points out that the Scottish Government was too optimistic with its oil forecasts for both last year and the current year. The SNP needs to publish its latest forecasts as a matter of urgency and explain what it would do in a separate Scotland if the OBR figures turned out to be accurate."
Scots LibDem leader Willie Rennie said: "This shows there is a £4.6bn black hole between the Scottish Government's most optimistic prediction and the OBR's prediction for oil revenues in the year the SNP would have Scotland leave the UK."
A Scottish Government spokesman said: "There is no doubt that Scotland can more than afford to become an independent country. As Standard and Poor's noted last week, even without North Sea oil and calculating per capita GDP only by looking at onshore income Scotland would qualify for their highest economic assessment."