Foreign Minister Guido Westerwelle will personally meet with US envoy John B. Emerson later Thursday, the spokesperson announced, in a highly unusual step between the decades-long allies.
"The American ambassador was summoned for talks with Foreign Minister Westerwelle this afternoon. The position of the German government will be presented clearly."
Merkel had called US President Obama on Wednesday demanding answers after learning US spies may have monitored her phone, warning this would be "breach of trust" between international partners.
The White House spokesperson said it is not now listening in on Merkel, but did not deny the possibility her communications may have been intercepted in the past.
The allegations sparked outraged in Germany and Merkel's spokesperson Steffen Seibert said in a statement that she "made clear that she unequivocally disapproves of such practices, should they be confirmed, and regards them as completely unacceptable".
She had demanded "an immediate and comprehensive explanation" from Washington, the statement said.
"Among close friends and partners, as the Federal Republic of Germany and the US have been for decades, there should be no such monitoring of the communications of a head of government," the statement added, indirectly citing Merkel's comments to Obama.
"This would be a serious breach of trust."
"Such practices must be stopped immediately," the German chancellor told Obama, the statement said.
German and US intelligence agencies cooperate closely on counter-terrorism efforts and other matters related to espionage.
But the latest revelations threatened the personal trust and close cooperation between Obama and Merkel, which saw the US leader pay a long-awaited visit to Berlin earlier this year.
Merkel grew up in communist East Germany, where state spying on citizens was common.
Germans also carry the trauma of mass abuses by the security services under the Nazi regime.
News of the eavesdropping suspicion and the German protest came first from Spiegel Online, whose parent magazine reported many of the US surveillance claims made by fugitive intelligence contractor Edward Snowden.
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the germans have now fallen to a level,where they cannot even protect the phone of their chancellor.