Some£6.5bn of EU funds are due over the next seven years, about half of which is not earmarked for specific places.
Britain will lose the money after 2013 because it will be diverted to the EU's new east European members.
The Centre for Cities has said the government should spend the money in the northern and midland cities best poised for growth, however.
'If we stick it into cities with the potential for growth that will pay long-term dividends.'
Daniel Dobson-Mouawad, chief executive of Pro-Manchester, which promotes the city's financial and professional sectors, said: 'At a time of constraints on government spending this money could be used to help close the productivity gap between north and south.
'It depends on whether the government wants to do that or prefers to play the geopolitical equity card by spreading the money among [poorer] areas.'
The earmarked£3.2bn is for former industrial areas in Merseyside and South Yorkshire and economically weak rural areas in Cornwall, Wales and Scotland.