The Department for Communities and Local Government has refused a European Commission offer to extend the 2000-06 European Regional Development Fund, which means the North West has lost £202m.
The extension would have enabled England's regions to spend up to £671m in unspent cash.
The extension was accepted by Scotland, Wales and Northern Ireland, which stand to gain between £25m and £60m.
DCLG officials reviewed the decision, raising expectations that the regions would be given the opportunity to bid for the cash and Brussels had indicated it would welcome a ministerial U-turn.
However, Government minister John Healey ruled out a reversal and said it would have been "difficult if not impossible" to spend the cash in the time allowed. He stated it was more important for the regions to focus on maximising the potential of the current 2007-13 ERDF round.
The unclaimed euros will now be taken off the UK's future contribution to the EU, so will effectively go into the Treasury's coffers rather than to projects in the regions.
Liberal Democrat deputy leader of Liverpool City Council, Cllr Flo Clucas, was reported saying it "could have been used to help businesses through the recession".