Germany's foreign minister, Guido Westerwelle, has called the US ambassador to a personal meeting to discuss allegations that US secret services bugged Angela Merkel's mobile phone.

The decision to call in John B Emerson, who has only been the US representative in Berlin since mid-August, is an unusually drastic measure. During previous upheavals in relations, such as over the Syrian crisis, conversations have taken place between diplomats.

Allegations that the US government's spying had reached the highest level were met with outrage and disappointment in Germany on Thursday. The country's defence minister, Thomas de Maiziere, told ARD television it would be bad if the reports turned out to be true. Washington and Berlin could not return to business as usual, he said.

Informed sources in Germany said Merkel was livid about the reports that the NSA had bugged her phone and was convinced, on the basis of a German intelligence investigation, that the reports were utterly substantiated.

The German news weekly, Der Spiegel, reported an investigation by German intelligence, prompted by research from the magazine, that produced plausible information that the chancellor's mobile was targeted by the US eavesdropping agency. She found the evidence substantial enough to call the White House and demand clarification.

The outrage in Berlin came days after the French president, François Hollande, called the White House to confront Barack Obama with reports that the NSA was targeting the private phone calls and text messages of millions of French people.

While European leaders have generally been keen to play down the impact of the whistleblowing disclosures in recent months, events in the EU's two biggest countries this week threatened an increasing lack of trust in transatlantic relations.

On Wednesday Merkel's spokesman, Steffen Seibert, made plain that the chancellor upbraided Obama unusually sharply and also voiced exasperation at the slowness of the Americans to respond to detailed questions about the NSA scandal since the Snowden revelations first appeared in the Guardian in June.

Merkel told Obama that "she unmistakably disapproves of and views as completely unacceptable such practices, if the indications are authenticated", Seifert said. "This would be a serious breach of confidence. Such practices have to be halted immediately."

The sharpness of the German complaint direct to a US president strongly suggested that Berlin had no doubt about the grounds for protest. Seibert voiced irritation that Berlin had waited for months for proper answers from Washington on the NSA operations.

On Thursday Süddeutsche Zeitung conveyed a strong sense of the depth of disillusionment with the US president in Germany when it wrote that "Barack Obama is not a Nobel peace prize winner, he is a troublemaker".

In a comment piece in the German broadsheet, Robert Rossmann wrote that during his last visit to Germany, "the American president had flamboyantly promised more trusting collaboration between the countries. Even Merkel seems to have lost faith in that promise by now. One doesn't dare imagine how Obama's secret services deal with enemy states, when we see how they treat their closest allies."

Die Zeit wrote that Obama's "half-hearted denial" of the allegations raised more questions than it answered. "Was Merkel's mobile the target of NSA surveillance in the past? … It is time for Obama and the US Congress to be ruthlessly transparent about the macabre practices of the NSA and restrain them strongly. They promised it months ago, but until recently very little has happened. With each revelation trust is eroded further. If America wants to stop annoying its friends and allies, it only has one option. Get on the front foot and be open."

Criticism was not focused solely on Obama, but was extended to Merkel, whose chief of staff only recently declared that the NSA scandal was finished. Many feel Merkel failed to react appropriately to the Snowden revelations, and was only stepping up the rhetoric now that she had been personally affected.

Germany's data protection commissioner, Peter Schaar, said that the reports showed "the absurdity of politicians trying to draw to a close the debate about surveillance of everyday communication here". He said it had been irresponsible of politicians not to be more upfront in calling for the US to clear up the matter.

Anke Domscheit-Berg, of the German Pirate party, told the Guardian: "In the past few months, Chancellor Merkel did very little to make the US government answer all those questions that should have had highest political priority. Now she gets a taste of what it feels like when foreign secret services spy on all your communication. We have stopped trusting empty promises and so should Angela Merkel. It is about time to get all dirty secrets on the table."

The debate in the coming days is likely to focus on how the allegations will affect new data protection regulation at the European level, with some MEPs calling for a Europe-only data cloud. In Frankfurter Allgemeine Zeitung, Georg Mascolo and Ben Scott warned of the creation of a "digital Maginot line" between Europe and the US, and instead called for a "no-spy treaty" between European countries.

"Storing data and surveillance would only be allowed for previously agreed goals – the fight against terrorism, the proliferation of weapons of mass destruction as well as grave acts of crime. All forms of political and economic espionage would be banned. The privacy of every EU citizen has to be respected by each EU secret service as if they were their own."