Scotland is set for a cut of about £250 million in European funding for growth investment and jobs over the next six years, the Scottish Government has claimed.
Ministers said the reduction in the EU budget fought for by Prime Minister David Cameron in Brussels would benefit the English, but the Scots would lose out.
They said the European Structural Fund budget for Scotland would be cut by 30 per cent for 2014-20 and Scotland would lose out because the new formula to be used to allocate the money favoured densely populated areas of the UK.
A spokesman for the UK government said that none of the budgets had yet been set.
The 2007-13 Structural Funds programmes in Scotland are worth about £730m, which has supported more than 250,000 people into employment and training and created more than 30,000 jobs.
The agreement reached earlier this month by EU leaders represented a 3.3 per cent cut from the previous seven-year budget, which was hailed as a victory for Mr Cameron.
The European Commission has not released regional allocation figures yet, but the Scottish Government estimates that the new formula will see cash fall to about £470m between 2014 and 2020.
Ms Sturgeon said: “The allocation of structural funds agreed to by EU member states, including the UK, could see Scotland face a disproportionate reduction in European structural funding.
“Although we expected reductions as a result of the overall reduction in EU spending, the allocations across the UK which are now emerging were not envisaged, significantly lower spending on encouraging investment, growth and jobs
would be extremely unwise in these difficult economic times.”
She continued: “Wales and Northern Ireland also face significant reductions, whilst England could receive an increase.
“I have made clear to the UK government that an allocation process that resulted in a disproportionate reduction for Scotland would be unacceptable, and I welcome the fact that the other devolved governments are also questioning the initial allocation.”
The Deputy First Minister added: “Michael Fallon, the UK minister for structural funds, has agreed that our officials will work together to identify alternative allocation methodologies to ensure the UK government recognises the importance of a fair allocation of funding.”
The UK government last night indicated that the final allocation of funding had yet to be set and that UK ministers would be working with the devolved administrations to make sure that allocations are fair.
A Scotland Office spokesman said: “The structural funds allocations within the UK for the next financial perspective have not been set. MFF (Multi-Annual Financial Framework) is a good result for the UK, in line with the position of SNP votes in Parliament in November. It will benefit UK taxpayers across the UK.
“Officials in Defra and BIS are working with Scottish Government officials on what this will mean for funds through CAP and Structural Funds.”
Ms Sturgeon’s comments came after it emerged that the SNP has appointed an expert on European law to help them engage with the EU in the run-up to the independence referendum.
Drew Scott, professor of EU studies at Edinburgh University, will advise on European treaties as they prepare to negotiate the terms of entry into the EU if Scotland votes Yes to independence.