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.