The French president sided with federalist Euro-MPs who are engaged in a bitter feud with Vaclav Klaus, the Czech president and a Eurosceptic.
Senior MEPs, including the president of the European Parliament, Hans Gert Poettering, caused a diplomatic incident ten days ago after demanding that Mr Klaus hoist the European flag over his residence during bad tempered talks in Prague.
"It was a wound, it was an outrage to see that flags had been taken down from public buildings," said President Sarkozy, the current holder of the EU's six-month rotating presidency which he hands over to the Czech Republic in January.
Yes, that dreary insistence that the EU flag must be flown everywhere, even where it's not wanted. The response is rather plain and simple:
Karel Schwarzenberg, the Czech foreign minister, hit back as the diplomatic war of words between Paris and Prague threatened to overshadow the smooth transfer of the EU presidency.
"There is no law binding the Czech Republic to hang the EU flag over Prague Castle. Prague Castle is a symbol of the Czech state and not the EU," he said.
"It is not up to the head of another state to criticise the Czech president over flags."
Quite. Whatever might be the ambition, the collapse of the nation states into a federal system, it hasn't actually happened yet. People are allowed to fly the 12 stars, but it's not required as yet. And Nigel Farage had something to say on it all:
Nigel Farage, the leader of UK Independence Party, compared the EU flag demand to the behaviour of Nazi or Soviet officials, both dictatorships that had occupied Prague and its Castle in the past.
"The manner in which Cohn-Bendit demanded that President Klaus fly the EU flag over his castle could easily have been done by a German official of over 70 years ago or a Soviet official of 20 years ago," he said.
"No doubt they think that Buckingham Palace should fly the EU flag to show its dominium."