The study said that for 2016-17 - which could be the first year of independence if there is a Yes vote in September's referendum - the highest estimates for both tax and spending "still suggests a shortfall between income and spend of around £4bn, or 6% of total spending".
But the research, by the Chartered Institute of Public Finance and Accountancy (CIPFA) Scotland, said in that year the UK could be facing an £82bn deficit - some 11% of total spending.
The report states: "Thus, the challenges facing an independent Scotland are not dissimilar to that of the UK in 2016-17.
"An independent Scotland could spend £69bn on public services in the proposed year of independence (2016-17), but estimated tax revenue is less than that.
"This means that there will be a shortfall to be met, but an independent Scottish Government would have the powers and financial levers necessary to manage its financial and economic position sustainably."
It stressed that a "clear and understandable picture of Scotland's public finances is essential to fully inform this important national debate" in the run up to the historic vote.
As part of that, CIPFA produced a "balance sheet" for the current devolved Scottish public sector.
CIPFA estimated that the devolved government and wider public sector to have assets of approximately £84.4bn, along with liabilities of approximately £100.7bn.
The report said it is "common for governments to have a negative equity position".
Don Peebles, head of CIPFA Scotland, said: "The decision the Scottish people are being asked to take is vitally important and needs to be supported by financial information.
"A balance sheet for the Scottish public sector would provide a starting point that would help voters to understand clearly what we know about where Scotland's finances are now, but also where further information needs to be provided.
"This report helps to shed light on the debate so as to better inform voters on all sides of the argument."