American Defence Secretary William Cohen told a meeting of Nato defence ministers in Brussels that too many questions about the planned rapid reaction force remained unanswered.
The UK Defence Secretary, Geoff Hoon described Mr Cohen's speech as very frank and robust.
The proposed 60,000-strong force has in general been warmly welcomed by Nato - many of whose members would be key contributors.
But the BBC defence correspondent, Jonathan Marcus, says the Americans and others feel that France - which is not part of Nato's integrated military structure - is pushing too hard for the EU to have a significant planning capability of its own.
Linking difficulties
Efforts to establish a clear framework for relations between Nato and the EU are bogged down over fears that the new European force could compromise Nato's cohesion.
Mr Cohen seemed frustrated that it was taking so long to establish clear and detailed institutional links between Nato and the EU.
Practical arrangements such as when the two organisations should meet and how often are still to be resolved.
Military planning remains a problem, with the British and Americans insisting that Nato should be at the heart of the planning effort.
Nato Secretary-General Lord Robertson has welcomed the EU initiative as something that will encourage the Europeans to bolster their military capabilities.
But he said that Mr Cohen was right to warn them, and urged the two sides to get the links correct.
Turkey's fears
It is not just the Americans who are worried.
The Turkish Government wants to participate fully in EU decision-making on security issues, especially if Nato assets are to be used in any operation - a demand which our correspondent says it will be hard for the Europeans to satisfy.
While provisional mechanisms are in place to enable the EU and Nato to compare notes on a variety of security-related issues, the final institutional arrangements are not yet in place.
These will have to be left until after the EU's Nice summit that begins on Thursday
.