Dr Angus Armstrong, of the National Institute of Economic and Social Research (NIESR), was speaking as a new set of papers on the economic impact of Scottish independence was published.
He also urged the UK Government to state clearly if a currency union with Scotland could be agreed in the event of a Yes vote in September's referendum.
Alex Salmond's Government in Edinburgh has put forward plans for Scotland to retain the pound if the country becomes independent, establishing a ''Sterling zone'' with the UK.
But UK ministers, including Chancellor George Osborne, have previously cast doubt on whether this is achievable, saying it is unlikely the UK Government would back such a move.
Dr Armstrong, the head of NIESR's macroeconomics and finance group, said that stance meant there was a "degree of uncertainty over this most important issue" which needed to be clarified.
Speaking at a press conference in Edinburgh, he said: "You want this, one way or another, settled."
He added: "We need to have a discussion about this. And the UK is able to have this discussion, it could say yes or no to a formal union.
"Having this degree of uncertainty over this most important issue, which could be clarified - either one way or the other it could be clarified - I don't think it's helping people."
Dr Armstrong also warned of possible "vulnerabilities" if there was a currency union between an independent Scotland and the rest of the UK, because of the level of debt the new nation could have.
The only way to avoid this would be if such a deal imposed "very tight controls across Scotland's tax and spending policy", he said.
A new paper from Dr Armstrong and Monique Ebell of NIESR estimated Scotland's share of the UK debt on independence could be £146 billion, based on its 8.4% share of the UK's population.
This would give Scotland a debt to GDP ratio of approximately 81%, according to the report.
Dr Armstrong said: "In my view that is a high debt ratio for any new, relatively small economy. Normally we think a debt to GDP ratio of about 40% are safe.
"We think there's vulnerabilities there."
He added: "With the level of debt we think would be a reasonable split, we think that would mean in an independent Scotland a form of currency union would be vulnerable.
"The only way to make it not vulnerable is to have fiscal transfers across nations, but then you would have very tight controls across Scotland's tax and spending policy."
Dr Armstrong said in these circumstances the "constraints could become so heavy you would have to ask 'is this independence?'."
He also stressed: "What would be key would be what are the prices for doing this, what constraints would the UK want?"
Ms Ebell, a research fellow at NIESR, pointed out an independent Scotland's debt to GDP level would be lower than that for the rest of the UK, but would be "quite high by historical standards".
She said: "A country with its own currency has full control over monetary policy, it can set interest rates as it pleases, it can engage in quantitative easing or not. In addition it is in control of its own fiscal policy, taxes can be set, spending can be set, without any explicit constraints."
But she added: "In a monetary union, particularly in a monetary union where the countries are of such radically different sizes such as Scotland and the rest of the UK - Scotland would be about one tenth the size of the rest of the UK - it is difficult to see how an independent Scotland would be able to yield much influence over monetary policy.
"So effectively Scotland would also be ceding control of monetary policy within a monetary union."
Their warning comes just over a week after Bank of England governor Mark Carney said for a currency union to be effective , a newly-independent Scotland would have to hand over some national sovereignty.
"A durable, successful currency union requires some ceding of national sovereignty," he said.
The research by Dr Armstrong and Ms Ebell is one of a series of papers focusing on the economic impact of independence published today in the latest National Institute Economic Review
Scottish Finance Secretary John Swinney said these papers showed that "Scotland is in a stronger fiscal position than the rest of the UK right now".
He added: "On any calculation an independent Scotland will have lower levels of debt than the rest of the UK and the firm foundations we need to build a stronger and fairer economy."
But he said: "The powers of independence are essential if we are to redress the economic balance and ensure Scotland's economy grows at the levels other small European nations have experienced.
"As these studies confirm, an independent Scotland will be able to take different policy and spending decisions that can change the path we are currently on as part of the UK.
"Remaining part of the UK will - as these reports highlight - see the Barnett formula which provides Scotland's funding cut by around £4 billion and see Scotland face the issues of an ageing population without the ability to grow our working age population, to attract new people to Scotland or to fully counter the economic pull of London that UK ministers acknowledge is damaging the wider economy.
"With a vote for independence we will finally be able to invest in transformational childcare, helping more people into the labour market and boosting the working age population. We would also be able to secure more investment, prevent high level jobs from relocating to London and create more opportunities for our young people. All of which will help to meet the challenges that Scotland faces whether or not we vote for independence."
Blair Jenkins, chief executive of the pro-independence campaign group Yes Scotland, said the reports showed "by whatever measure is used, Scotland has got what it takes to be a successful and prosperous independent country".
He added: "Scotland is already in a stronger financial position than the rest of the UK and, with our own future in our own hands, we have all the ingredients to create the kind of fairer, more socially just country that most Scots want."
But Blair McDougall, campaign director for the pro-UK Better Together group, said: "Expert after expert are lining up to point out the enormous challenges we would face if we lose the financial back-up of being part of one of the biggest economies in the world.
"From funding our vital public services, to servicing our debt and paying our pensions in the future, each one of these papers says that Scotland would be worse off without the economic security of the UK."
He added: "Economists have rounded on Salmond's reckless threat to default on Scotland's debt if he doesn't get his Eurozone style currency union. People understand that refusing to pay your debts means paying more to borrow money. The same is true for Scotland if Salmond leaves us with a bad credit rating.
"The report on pensions makes clear that the SNP plan to pay pensions earlier means cutting pensions. This comes just days after Scotland's accountants warned that there was no real plan for paying pensions after independence.
"Over the past week Alex Salmond has refused to listen to what experts and business leaders are telling him. No doubt he will do the same with these reports."
Meanwhile Scottish Liberal Democrat leader Willie Rennie said: "This analysis confirms that the future is deeply uncertain. The academics have pointed to higher tax, unaffordable policies and depleting oil income.
"The uncertainty of independence contrasts starkly with the progress we've making in the UK with cuts to taxes, increases in pensions, more jobs and expanded nursery education."