Angela Merkel told the US President to remain patient after Wilbur Ross, the US commerce secretary, warned Mr Trump was growing frustrated with the lack of progress.
Speaking in Brussels, the German Chancellor claimed talks between the US and EU compared with other negotiations have not “yet taken so long”.
She said: “Well let me say first that I am quite happy first and foremost that these talks are taking place.
“That these talks will not be easy, something that I think was clear to all.
“I think these talks ought to be continued, if we measure it with other trade talks and their duration then they haven’t yet taken so long.”
The European Union’s trade deal with Canada took seven years to negotiate and to come into effect.
The US commerce secretary highlighted Mr Trump’s growing frustrations over trade between the US and the EU when he spoke in Brussels.
Mr Ross said: “The president’s patience is not unlimited”.
The US President has already warned the European Union about placing tariffs on their car exports.
He said: “The European Union is possibly as bad as China, only smaller.
“They send a Mercedes in, we can’t send our cars in.”
Speaking earlier this month, the US President said the threat of tariffs has pushed Brussels, Japan and South Korea to seek out new trade agreements with the US.
He said: “If we can’t make a deal with the European Union, we will respectfully put tariffs on cars.”
Mr Trump insists his protectionist trade policies are leading to better deals for the US.
He said: “Without tariffs we wouldn’t be talking about a deal.”
The US has already placed tariffs on imports of EU steel and aluminium while Brussels has retaliated with tariffs on US goods. Negotiators agreed in July to not step up their dispute.