"The thing we always have to keep in mind when we are working together is if the person across the table is possibly working at the same time for someone else, that for me isn't a trusting relationship," she told German ZDF television in a pre-recorded interview.
"Here we obviously have different points of view and we need to talk to one another," Merkel said, adding that she had "naturally hoped for a change" in Washington's behaviour.
White House spokesman Josh Earnest, who previously declined to go into detail about the row because it touched on intelligence matters, offered a window into US thinking.
"Allies with sophisticated intelligence agencies like the United States and Germany understand with some degree of detail exactly what those intelligence relationships and activities entail," Earnest said.
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"Any differences that we have are most effectively resolved through established private channels, not through the media."
Some US officials have privately expressed frustration with Germany's angry reaction to the reported discovery that two government officials were working for the CIA and its decision to respond in a highly public manner by expelling the spy agency's Berlin chief -- an unusual display of fury by Germany towards its ally.
"We no longer live in the Cold War era where everyone is suspicious of everyone. I think the secret services in the 21st century should concentrate on important issues," Merkel said. "We work very closely with the Americans and I hope that will continue."
She repeated however that the espionage affair would not jeopardise negotiations between Berlin and Washington over a transatlantic trade deal.
German Foreign Minister Frank-Walter Steinmeier reacted to the scandal by saying he wanted a revived partnership with Washington, based on "trust and mutual respect".