office with US envoy John B. Emerson that Washington provide straight answers on the allegations immediately, saying the health of the relationship was at stake.
"For us, spying on close friends and partners is totally unacceptable. This undermines trust and this can harm our friendship," he told reporters in German then in English.
"We need the truth now."
The ministry could not confirm that the summons was unprecedented in US-German post-war relations but it was seen as a highly unusual move between the close allies.
Earlier Merkel, heading into a European Union summit in Brussels where the growing spy scandal has hijacked the agenda, had expressed her anger over the latest reports.
"Spying between friends, that's just not done," Merkel said.
Federal prosecutors said they would launch an investigation as to whether German laws had been broken while a parliamentary committee said it would re-open a probe of the matter.
A member of the committee said that a delegation of MPs would head to Washington soon on a fact-finding mission, following media reports that US officials met with Merkel's staff in Berlin Wednesday before the allegations were made public.
Merkel had called US President Barack Obama Wednesday demanding answers after learning US spies may have monitored her phone, warning this would be "breach of trust" between international partners.
A White House spokesman said it is not now listening in on Merkel, but did not deny the possibility her communications may have been intercepted in the past.
Reports said that the alleged tapping targeted not Merkel's official mobile phone but a separate device she uses for conducting business for her Christian Democratic Union party.
German and US intelligence agencies cooperate closely on counter-terrorism efforts and other matters related to espionage.
But the latest revelations threaten 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.
As the NSA scandal raged in Germany during the campaign for the September election, Obama indicated that his personal ties with Merkel meant he had no need to spy on her.
"If I want to know what Chancellor Merkel is thinking, I will call Chancellor Merkel," he said in July.
Merkel grew up in communist East Germany, where state surveillance of citizens was rampant. Germans also carry the trauma of mass abuses by the security services under the Nazi regime.
The conservative daily Die Welt called the alleged snooping a "diplomatic bomb" and "a punch in the face of German security agencies", while a Sueddeutsche Zeitung headline labelled it "the worst imaginable insult".
"The Americans are and remain our best friends but that is not on," Defence Minister Thomas de Maiziere told ARD public television.
"I have assumed for years that my mobile phone is being tapped but I didn't suspect the Americans."
However the opposition Greens party attacked Merkel's government itself for having declared the NSA spying scandal -- centred on charges of surveillance of millions of citizens' phone calls, emails, chats and other communications -- effectively over several months ago.
"It's scandalous that the government appeased and obscured throughout the entire NSA affair, but that now, when it comes to confidentiality of communications of the chancellor, Merkel voices personal indignation in a phone call to the American president," Greens lawmaker Konstantin von Notz said.
"Now we're seeing the protest that was missing when the population was being spied on," Die Welt said.
Merkel had offered assurances during her campaign for a third term -- which she handily won last month -- that she had taken up the most serious allegations of mass NSA spying with Washington and was confident she would receive a complete answer.
She stressed then that US intelligence had helped prevent terror attacks on German soil.