Barack Obama has sought to address European concerns over internet privacy in the wake of the National Security Agency surveillance scandal, insisting US authorities are not "rifling through the emails" of ordinary people and he is confident the US intelligence services have "struck the appropriate balance" between security and civil rights.

"I was a critic of the previous administration for those occasions in which I felt they had violated our values and I came in [to office] with a healthy scepticism about how our various programmes were structured," Obama told the press conference in Berlin's chancellery. But, he added, having examined how the US intelligence services were operating: "I'm confident that at this point we have struck the appropriate balance".

Obama's remarks on the NSA dominated the 45-minute press conference, which also covered Syria, the global economic crisis and Guantánamo, with observers suggesting he had used the occasion as an opportunity to confront European scepticism over the US government's attempts to justify their surveillance operations, which have triggered deep concerns both at home and abroad.

In Germany the practices have widely been compared to those of the Gestapo and Stasi, the state intelligence arms that operated during the Nazi and communist dictatorships. Questions surrounding them have dominated the runup to the Obama family's 25-hour visit to the German capital, which comes almost exactly 50 years after John F Kennedy flew into the city and delivered his legendary "Ich bin ein Berliner" speech.

In what came across as something of a charm offensive, Obama even went into a degree of detail over the way the NSA's programme worked, saying he wanted to be very specific about the programmes that "have caused so much controversy".

"Essentially one programme allows us to take a phone number that has been discovered … through some lead that is typical of what our intelligence services do. And what we try to discover is has anybody else been called from that phone." He stressed that initially no check on content took place. "Nobody's listening in on the conversation at that point – it's just determining whether or not if for example we found a phone number in Osama bin Laden's compound after the raid, had he called anybody in New York or Berlin." But from that point, to listen in to the conversation a court's permission would have to be sought, he insisted, adding that the process applied only "very narrowly to leads that we have obtained on issues related to terrorism or proliferation of weapons of mass destruction".

He added: "This is not a situation in which we are rifling through the ordinary emails of German citizens or American citizens or French citizens or anybody else. This is not a situation where we simply go into the internet and start searching any way that we want. This is a circumscribed, narrow system, directed at us being able to protect our people and all of it is done with the oversight of the courts."

Delivering his six-minute defence as a staid Angela Merkel, the German chancellor, looked on, Obama concluded by saying the procedure had saved lives. "We know of at least 50 threats that have been averted because of this information not just in the United States, but in some cases threats here in Germany. So lives have been saved, and the encroachment on privacy has been strictly limited by a court-approved process to relate to these particular categories," he said.

Merkel responded with a distinct air of scepticism, saying it was a reflection of German concerns that she and Obama had discussed the issue "at length and in great depth".

"People have concerns precisely about there having possibly been some kind of across-the-board gathering of information," she said. "The unanswered questions – and of course there are a few – we will continue to discuss." She acknowledged that information received by US authorities had helped foil an Islamist terrorist plot in the Sauerland region of Germany in 2007.