On Wednesday the prime minister pledged to hold a in or out referendum should the Conservatives win the next election in 2015.
But the Lib Dem leader said his current coalition partner was wrong to make the commitment. "My priority is to build a stronger economy in a fairer society," he said.
"That job is made all the harder if we have years of grinding uncertainty because of an ill-defined protracted negotiation of Britain's status within the EU. That's why in my view it is not in the national interest."
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The deputy prime minister and his Lib Dem cabinet colleagues have sided with Ed Miliband over the issue of a referendum, warning it will damage the country's fragile economic recovery.
Clegg added: "There is the right time and right place for a referendum. My view is, years and years of uncertainty because of protracted ill-defined renegotiating is not in the national interest, it hits growth and jobs."
But he said it was for Cameron to set out what he wanted to put in the next Conservative manifesto in an effort to win a majority.
Cameron has said that if he is still prime minister after 2015, whether in coalition or as the leader of a majority Conservative government, a referendum "will happen" - suggesting it will be a 'red line' in any negotiations with the Lib Dems.
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