"We could better develop our economies, stimulate growth, more jobs, if we didn't have so many obstacles in our talks," Merkel said in her weekly video podcast.
The chancellor was speaking on the 60th anniversary of Germany's Atlantic Bridge association, which aims to promote trade, military and educational relations between Washington and Berlin.
The organisation called for "a greater collaboration" between the two countries in the field of technology.
The relationship between the two countries was "a pillar of German politics and will remain so in the future," said Merkel.
“Politically we have a close relationship. We have a great responsibility to the world. We fight for human rights together."
But the two nations still had great differences of opinion, Merkel added, particularly on the issue of climate change where "Germany could be an example" to the US.