The prospects for a new trade pact between the US and the European Union worth hundreds of billions have suffered a severe setback following allegations that Washington bugged key EU offices and intercepted phonecalls and emails from top officials.

The latest reports of NSA snooping on Europe – and on Germany in particular – went well beyond previous revelations of electronic spying said to be focused on identifying suspected terrorists, extremists and organised criminals.

The German publication Der Spiegel reported that it had seen documents and slides from the NSA whistleblower Edward Snowden indicating that US agencies bugged the offices of the EU in Washington and at the United Nations in New York. They are also accused of directing an operation from Nato headquarters in Brussels to infiltrate the telephone and email networks at the EU's Justus Lipsius building in the Belgian capital, the venue for EU summits and home of the European council.

Without citing sources, the magazine reported that more than five years ago security officers at the EU had noticed several missed calls apparently targeting the remote maintenance system in the building that were traced to NSA offices within the Nato compound in Brussels.

The impact of the Der Spiegel allegations may be felt more keenly in Germany than in Brussels. The magazine said Germany was the foremost target for the US surveillance programmes, categorising Washington's key European ally alongside China, Iraq or Saudi Arabia in the intensity of the electronic snooping.

Germany's justice minister, Sabine Leutheusser-Schnarrenberger, called for an explanation from the US authorities. "If the media reports are true, it is reminiscent of the actions of enemies during the cold war," she was quoted as saying in the German newspaper Bild. "It is beyond imagination that our friends in the US view Europeans as the enemy."

France later also asked the US authorities for an explanation. France's foreign minister, Laurent Fabius, said: "These acts, if confirmed, would be completely unacceptable.

"We expect the American authorities to answer the legitimate concerns raised by these press revelations as quickly as possible.".

Washington and Brussels are scheduled to open ambitious free trade talks next week following years of arduous preparation. Senior officials in Brussels are worried that the talks would be overshadowed by the latest disclosures of US spying on its closest allies.

"Obviously we will need to see what is the impact on the trade talks," said a senior official in Brussels. A second senior official said the allegations would cause a furore in the European parliament and could then hamper relations with the US.

Robert Madelin, one of Britain's most senior officials in the European commission, tweeted that EU trade negotiators always operated on the assumption that their communications were listened to.

A spokesman for the European commission said: "We have immediately been in contact with the US authorities in Washington and in Brussels and have confronted them with the press reports. They have told us they are checking on the accuracy of the information released yesterday and will come back to us."

There were calls from MEPs for Herman Van Rompuy, the president of the European council – who has his office in the building allegedly targeted by the US – and José Manuel Barroso, the president of the European commission, to urgently appear before the chamber to explain what steps they were taking in response to the growing body of evidence of US and British electronic surveillance of Europe through the Prism and Tempora operations.

Guy Verhofstadt, the former Belgian prime minister and leader of the liberals in the European parliament, said: "This is absolutely unacceptable and must be stopped immediately. The American data collection mania has achieved another quality by spying on EU officials and their meetings. Our trust is at stake."

Luxembourg's foreign minister, Jean Asselborn, told Der Spiegel: "If these reports are true, it's disgusting." Asselborn called for guarantees from the very highest level of the US government that the snooping and spying is immediately halted.

Martin Schulz, the head of the European parliament, said: "I am deeply worried and shocked about the allegations of US authorities spying on EU offices. If the allegations prove to be true, it would be an extremely serious matter which will have a severe impact on EU-US relations.

"On behalf of the European parliament, I demand full clarification and require further information speedily from the US authorities with regard to these allegations."

There were also calls for John Kerry, the US secretary of state, to make a detour to Brussels on his way from his current trip to the Middle East, to explain US activities.

"We need to get clarifications and transparency at the highest level," said Marietje Schaake, a Dutch liberal MEP. "Kerry should come to Brussels on his way back from the Middle East. This is essential for the transatlantic alliance. The US can only lead by example, and should uphold the freedoms it claims to protect against attacks from the outside. Instead we see erosion of freedoms, checks and balances, from within."

Within senior circles in Brussels, however, it has long been assumed that the Americans were listening to or seeking to monitor EU electronic traffic.

"There's a certain schadenfreude here that we're important enough to be spied on," said one of the officials. "This was bound to come out one day. And I wouldn't be surprised if some of our member states were not doing the same to the Americans."

The documents suggesting the clandestine bugging operations were from September 2010, Der Spiegel said.

A former senior official in Brussels maintained that EU phone and computer systems were almost totally secure but that no system could be immune to persistent high-quality penetration operations.

"I have always assumed that anyone with a decent agency was listening, hacking if they could be bothered," he said. "It doesn't bother me much. Sometimes it's a form of communication."

Der Spiegel quoted the Snowden documents as revealing that the US taps half a billion phone calls, emails and text messages in Germany a month. "We can attack the signals of most foreign third-class partners, and we do it too," Der Spiegel quoted a passage in the NSA document as saying.

On an average day, the NSA monitored about 20m German phone connections and 10m internet datasets, rising to 60m phone connections on busy days, the report said.

Officials in Brussels said this reflected Germany's weight in the EU and probably also entailed elements of industrial and trade espionage. "The Americans are more interested in what governments think than the European commission. And they make take the view that Germany determines European policy," said one of the senior officials.

Jan Philipp Albrecht, a German Green party MEP and a specialist in data protection, told the Guardian the revelations were outrageous. "It's not about political answers now, but rule of law, fundamental constitutional principles and rights of European citizens," he said.

"We now need a debate on surveillance measures as a whole looking at underlying technical agreements. I think what we can do as European politicians now is to protect the rights of citizens and their rights to control their own personal data."

Talking about the NSA's classification of Germany as a "third-class" partner, Albrecht said it was not helping to build the trust of Germans or other Europeans. "It is destroying trust and to rebuild that, [the US] will need to take real action on legislation," he said.

Meanwhile, it has emerged that at least six European member states have shared personal communications data with the NSA, according to declassified US intelligence reports and EU parliamentary documents.

The documents, seen by the Observer, show that – in addition to the UK – Denmark, the Netherlands, France, Germany, Spain, and Italy have all had formal agreements to provide communications data to the US. They state that the EU countries have had "second and third party status" under decades-old signal intelligence (Sigint) agreements that compel them to hand over data which, in later years, experts believe, has come to include mobile phone and internet data.

Under the international intelligence agreements, nations are categorised by the US according to their trust level. The US is defined as 'first party' while the UK, Canada, Australia and New Zealand enjoy 'second party' trusted relationships. Countries such as Germany and France have 'third party', or less trusted, relationships.

The data-sharing was set out under a 1955 UK-USA agreement that provided a legal framework for intelligence-sharing that has continued.

It stipulates: "In accordance with these arrangements, each party will continue to make available to the other, continuously, and without request, all raw traffic, COMINT (communications intelligence) end-product and technical material acquired or produced, and all pertinent information concerning its activities, priorities and facilities."

The agreement goes on to explain how it can be extended to incorporate similar agreements with third party countries, providing both the UK and the US agree.

Under the third party data-sharing agreements each country was given a codename. Denmark was known as Dynamo while Germany was referred to as Richter. The agreements were of strategic importance to the NSA during the cold war.

However, Simon Davies, an intelligence expert and project director at the London School of Economics who writes the Privacy Surgeon blog, suggested the NSA's role had been given a sharper focus following amendments to the US Foreign Intelligence Surveillance Act (Fisa).

In an interview published in full last night on Davies' blog, former NSA director General Michael Hayden said: "The changes made to Fisa in 2008 were far more dramatic – far more far-reaching than anything President Bush authorised me to do."

Davies told the Observer that confirmation of the secret agreements showed there was a need for the EU to investigate.

"It's clear that the European parliament must intervene at this point through a public inquiry," Davies said. "MEPs should put the interests of their citizens above party politics and create meaningful reforms."

The covert data-sharing relationship between leading European countries and the US was first outlined in a 2001 report by the European parliament.

The report stated: "Germany and the United Kingdom are called upon to make the authorisation of further communications interception operations by US intelligence services on their territory conditional on their compliance with the ECHR (European Convention on Human Rights)."