The row broke out as European Union defence ministers met in Bratislava to discuss ways of boosting defence cooperation, one of the priorities set when the bloc's leaders met without Britain earlier this month.
Arriving for the talks, British defence minister Michael Fallon said NATO - which shares 22 of its 28 members with the EU - had to remain a "cornerstone of our defence and the defence of Europe".
Asked whether Britain could veto the plans in the estimated two-plus years before it formally leaves the EU, Fallon replied: "There is no majority here for a EU army.
"There are a number of other countries who believe with us that cuts across the sovereignty of individual nation states."
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But NATO Secretary General Jens Stoltenberg appeared to contradict Fallon's claims.
"There is no contradiction between strong European defence and strong NATO, actually it reinforces each other," said Stoltenberg, who was also attending today's meeting of the EU ministers.
Mogherini said the EU defence ministers had "found common ground... On the need to strengthen European defence cooperation, and in full complementarity with NATO".
Citing an EU-NATO agreement signed in Warsaw in July, she said it would be "in full complementarity with no duplications, but mutually reinforcing our work".
EU leaders on September 16 agreed at a summit in Bratislava on a six-month roadmap to create a new "vision" for the EU following the shock June 23 British vote to leave.
Britain, which along with France is one of the EU's two biggest defence powers, has always opposed any common European defence force on the grounds that it would double up with NATO.
The EU's plans are also being watched warily in many Eastern European nations that depend on NATO's security umbrella more than ever in the face of a resurgent Russia.
The issue is also at stake in the US presidential election, where Republican candidate Donald Trump has openly raised questions about the alliance's key Article 5 collective security guarantee.
"We are leaving the European Union but we remain committed to the security of Europe and putting more troops into Estonia or Poland next year.