Ahead of a special debate on US secret-service snooping on German soil which included her mobile phone, Merkel kicked off a statement to parliament meant to tackle another issue by addressing the US espionage claims.
"The transatlantic relationship and therefore also the negotiations for a free-trade agreement are presently without doubt being put to the test by the remaining accusations against the US and the collection of millions of data," Merkel told MPs.
Merkel, who went on to speak about EU partnerships with Eastern European nations, did not directly mention the surveillance of her phone.
But she stressed that the relationship with the US was of "paramount" importance for Germany and Europe.
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Lawmakers called a special parliamentary debate on the revelations that have put the US in the firing line and strained diplomatic ties, also casting a shadow over EU-US talks on what would be the world's biggest free-trade accord.
With US President Barack Obama's June visit to Berlin still fresh in many minds, deputies will examine the impact on US-German ties of sweeping surveillance, revealed in leaked US National Security Agency (NSA) documents.
And they will likely hear calls for Germany to grant asylum to Edward Snowden, the former NSA contractor who is behind the leaks that have fed near-daily media reports for months and is wanted in the US on criminal charges.
"Granting him asylum wouldn't be about revenge or retaliation for spying on us. It would be a decision based on our fundamental values -- and a moral duty," he wrote in a New York Times editorial.