The 89-year-old British monarch, who was at a state banquet in Berlin as part of a four-day visit to Germany, said that "division in Europe is dangerous".
Her speech yesterday was made in the presence of German Chancellor Angela Merkel and Prime Minister David Cameron, who wants to reform the UK's EU membership.
Buckingham Palace, however, stressed the comments were not about Cameron's EU aims.
"We have witnessed how quickly things can change for the better. But we know that we must work hard to maintain the benefits of the post-war world.
"We know that division in Europe is dangerous and that we must guard against it in the west, as well as in the east, of our continent. That remains a common endeavour."
Later a Buckingham Palace aide said: "This is not about the EU. The Queen is apolitical. She would never make a political point."
He said the EU was facing "major challenges" and that "an effective European Union" was "based on a stable foundation of shared values".
"As a good partner, Germany will support this dialogue. For Britain is part of Europe. The European Union needs Britain. A united Europe, a strong European Union, represent stability, peace and freedom -- for us all," he said.
Cameron has said in his election pledge he wants to reform the UK's membership of the EU before holding an in/out referendum in 2017.
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