A new report from Glasgow University's CPPR think tank says falling oil revenues will leave Scotland £5.3 billion in the red in 2018/19 - the year the UK as a whole is predicted to return to the black.
It came as Archie Norman, the chairman of ITV and former Conservative MP, claimed the SNP had no economic strategy for an independent Scotland and called on business leaders to speak out against a Yes vote in September's referendum.
In another blow to First Minister, the world's biggest fund manager, BlackRock, warned an independent Scotland's credit rating would be damaged, pushing up mortgage and credit card costs for ordinary consumers.
However, Nationalists were cheered by a poll that suggested earlier economic warnings about independence had failed to dent growing support for a Yes vote.
The ICM Research survey showed the Yes campaign catching up significantly in the referendum race, with support for independence rising two points to 39% while backing for a No vote fell.
The CPPR's report follows downgraded forecasts for North Sea oil revenues that were published alongside the Budget last week.
It calculates that Scotland's deficit - the gap between public spending and government income - will be worse in Scotland than the rest of the UK every year from now to 2018/19.
In the current financial year Scotland will be worse off by £750 per person.
The difference rises to £1060 in 2016/17, the year Mr Salmond aims to declare independence, and remains more than £1000 every year until 2018/19, the last year of the forecast.
In 2018/19, Scotland will be £5.3bn in the red while the UK as a whole expects to eliminate the deficit and return a modest surplus of £5bn.
The drop in oil revenues reverses recent deficit figures that showed Scotland's finances were in a healthier state than the UK's. The past figures have been widely used by the SNP to claim an independent Scotland would be better placed to maintain public spending.
The CPPR also called on the Scottish Government to update its own oil revenue forecasts after the latest downgrading by the Office for Budget Responsibility.
Economist John McLaren said: "Based on the OBR's latest forecasts, Scotland's fiscal position relative to the UK, continues to worsen.
"We now need the Scottish Government to update its own alternative North Sea oil tax scenarios based on the latest information available, in order to judge how these might affect Scotland's future fiscal balance."
The latest poll suggested many voters were unconcerned by economic warnings about independence. The ICM survey - conducted last week after a number of big firms said they saw a Yes vote as a risk - put backing for Yes on 39%, up two points compared with last month.
Support for staying in the UK fell from 49% to 46% while the proportion of voters undecided rose by a single point to 15%.
The findings prompted Scotland's leading polling expert Professor John Curtice to declare: "The No side is beginning to look like a campaign in trouble.
"Frightening voters with messages of economic doom and gloom is not working."
Blair Jenkins, chief executive of the Yes Scotland campaign, said: "With this poll, a swing of only around four points is all it takes to put Yes ahead -which we are confident of achieving - and we'll continue to step up our campaign work in all of Scotland's communities in the months ahead."
A spokesman for the pro-UK Better Together campaign said: "While we can take comfort from the fact that this poll, like all others, show that a clear majority of us want to remain in the UK, we need to make sure that we are fighting for every vote between now and September."