William Hague told the EUobserver following a meeting of foreign ministers in Brussels that the United Kingdom would not support a permanent operational HQ.
"We will not agree to it now and we will not agree to it in the future," Hague said, adding that a permanent military headquarters would duplicate NATO structures and would be a "waste of money."
The proposal was contained in a report by Baroness Catherine Ashton of Britain who is serving as the EU's high representative for foreign affairs and security policy.
Ashton told a news conference Hague's position did not come as a surprise.
"This is the same position as the previous British government," she said. "I am conscious you can't do much when unanimity of member states is required."