President Trump had told CBS News, "I think the European Union is a foe, what they do to us in trade".
He added: "You wouldn't think of the European Union, but they're a foe".
"I think she made one very catastrophic mistake and that was taking all of these illegals (sic), you know taking all of the people from wherever they come from", Trump said in a joint interview published by German daily Bild and British newspaper The Times, referring to Merkel's open-door policy for refugees fleeing war and persecution.
The President added that "Russia is a foe in certain respects. China is a foe economically, certainly they are a foe", said Mr Trump.
"It doesn't mean anything", he continued. But that doesn't mean they're bad.
"Tell us where you're going to extradite those folks", said Representative Trey Gowdy, who chaired a raucous House investigative hearing on Thursday that highlighted bitter, partisan divisions within the U.S. Congress over a probe of Russian election meddling that has clouded Trump's presidency.
Mr Trump said he respects Europe's leaders but says they have taken advantage of the United States on trade and defence spending. "Terrible. We'll stop that", Trump said during a North Atlantic Treaty Organisation leaders summit, according to German news magazine Der Spiegel, which cited sources at the alliance's meeting.
"America and the European Union are best friends", Tusk wrote.
In fact, Trump's father was born in New York City.
EU Council President Donald Tusk said anyone calling the EU foes was spreading "fake news". "Because it's like, what, are they waving a white flag?"
Trump recently took aim at North Atlantic Treaty Organisation on Twitter before saying last week in a meeting with other North Atlantic Treaty Organisation leaders that Moscow controlled Berlin because of an energy pipeline project.
Speaking ahead of his summit meeting on Monday with Russian President Vladimir Putin and after a tumultuous week in Europe, Trump said that European leaders were taking advantage of the US and failing to boost defense spending despite demands from Washington.