According to German media reports, Donald Trump had condemned Germany for "very bad" trade policies during a meeting with Mr Juncker, signalling he might take steps to limit sales of the country's cars in the United States.
Mr Juncker called the reports in Spiegel Online and Sueddeutsche Zeitung exaggerated, saying that while Mr Trump had talked about Germany's trade surplus as a problem, he had not done so aggressively.
But at a Group of Seven summit in Sicily today, White House economic adviser Gary Cohn said: "[Donald Trump] said they're very bad on trade, but he doesn't have a problem with Germany."
Mr Cohn said Mr Trump had pointed out during the meeting with Mr Juncker and Donald Tusk that his father had German roots in order to underscore the message that he had nothing against the German people.
Mr Trump's spokesman Sean Spicer also said the US President had "tremendous respect" for Germany and had only complained about unfair trade practices in the meeting.
Earlier on, the European Commission President Mr Juncker was quick to defend ally and German Chancellor Angela Merkel as the G7 group braces itself for trade talks with the US.
The Brussels bigwig said the United States cannot compare trade surplus to the European Union.
The US cannot compare their trade situation to the EU
Mr Juncker said: “I don’t want to comment but I have to comment.
“We had the meeting with President Trump which was frankly constructive. It’s not true that President Trump took an aggressive approach when it came to German surplus.
“The US cannot compare their trade situation to the EU. They have to compare with global performances of EU and I made it clear the European Commission is in charge of dealing with trade issues not member states.”
AFP GETTY/ EU
Donald Trump was warned not to compare trade surplus to EU, by Jean-Claude Juncker
Frosty- Angela Merkel greets Donald Trump at the G7 summit
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Mr Trump, when asked by reporters in Taormina whether he had accused Germany of being "very bad" on trade, did not respond.
A spokesman for the German government insisted Germany's trade surplus is "neither good nor evil”.
Government spokesman Georg Streiter said: ”It is the result of the interplay of supply and demand on global markets."
European Council President Donald Tusk said he did not want to comment on the row.
European Commission President Jean-Claude Juncker was quick to defend ally Angela Merkel
Donald Trump has warned the US will impose a border tax
He said: “I don’t want to be part of this new political culture of permanent leaks. My impression of today’s diplomacy is it needs professional plumbers rather than indiscreet diplomats. I don’t want to comment on leaks.”
Tensions have escalated between Berlin and Washington over Mr Trump’s proposed border tax and Germany's £43billion trade surplus amid concerns of a trade war between the two nations.
Mr Trump has warned the US will impose a border tax of 35 per cent on cars that German carmaker BMW plans to build at a new plant in Mexico and export to the US market.
NATO countries' heads of states gather in Brussels
Thu, May 25, 2017
NATO countries' heads of states and governments gather in Brussels for a one-day meeting
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U.S. President Donald Trump and Britain's Prime Minister Theresa May react during a ceremony at the new NATO headquarters in Brussels
The US is Germany's biggest export destination, buying German goods and services worth £93billion last year while exporting just £50billion worth in return.
It is Germany's third-largest trading partner, just behind China and France.
Mr Trump is attending his first major international summit but it not the only G7 newcomer. French President Emmanuel Macron, Italian Prime Minister Paolo Gentiloni and British Prime Minister Theresa May will also be attending the elite club for the first time.