• Unicef and Médecins du Monde were on surveillance list • Targets went well beyond potential criminals and terrorists • Revelations could cause embarrassment at EU summit

British and American intelligence agencies had a comprehensive list of surveillance targets that included the EU's competition commissioner, German government buildings in Berlin and overseas, and the heads of institutions that provide humanitarian and financial help to Africa, top-secret documents reveal.

The papers show GCHQ, in collaboration with America's National Security Agency (NSA), was targeting organisations such as the United Nations development programme, the UN's children's charity Unicef and Médecins du Monde, a French organisation that provides doctors and medical volunteers to conflict zones. The head of the Economic Community of West African States (Ecowas) also appears in the documents, along with text messages he sent to colleagues.

The latest disclosures will add to Washington's embarrassment after the heavy criticism of the NSA when it emerged that it had been tapping the mobile phone of the German chancellor, Angela Merkel.

One GCHQ document, drafted in January 2009, makes clear that the agencies were targeting an email address listed as belonging to another important American ally – the "Israeli prime minister". Ehud Olmert was in office at the time.

Three further Israeli targets appeared on GCHQ documents, including another email address understood to have been used to send messages between the then Israeli defence minister, Ehud Barak, and his chief of staff, Yoni Koren.

Prominent names that appear in the GCHQ documents include Joaquín Almunia, a Spaniard who is vice-president of the European commission with responsibility for competition policy.

Britain's targeting of Germany may also prove awkward for the prime minister, David Cameron: in October, he endorsed an EU statement condemning NSA spying on world leaders, including Merkel.

They have both been in Brussels, attending an EU summit that concludes on Friday.

The names and details are the latest revelations to come from documents leaked by the whistleblower Edward Snowden. They provoked a furious reaction from the European commission, Almunia and others on the target lists.

• The commission said the disclosures "are unacceptable and deserve our strongest condemnation. This is not the type of behaviour that we expect from strategic partners, let alone from our own member states." Almunia said he was "very upset" to discover his name was on GCHQ documents.

• Leigh Daynes, UK executive director of Médecins du Monde, said he was "bewildered by these extraordinary allegations of secret surveillance. Our doctors, nurses and midwives are not a threat to national security. There is absolutely no reason for our operations to be secretly monitored."

• Another target, Nicolas Imboden, the head of an NGO that provides help to African countries, said the spying on him was "clearly economic espionage and politically motivated".

• Human Rights Watch, Privacy International and Big Brother Watch condemned the targeting.

• Labour said the committee that oversees GCHQ should be given extra powers.

The disclosures reflect the breadth of targets sought by the agencies, which goes far beyond the desire to intercept the communications of potential terrorists and criminals, or diplomats and officials from hostile countries. Asked about this activity, a spokesman for GCHQ said it was "longstanding policy that we do not comment on intelligence matters", but the official maintained the agency "takes its obligations under the law very seriously".

The new information is published after a joint investigation by the Guardian, the German news magazine Der Spiegel and the New York Times. According to documents, the targeting efforts involved programmes run from GCHQ's listening post near the small Cornish seaside resort of Bude. This is a key listening facility that receives substantial funding from the NSA to undertake shared transatlantic surveillance operations.

Among other activities, the base was tasked with monitoring satellite communications between Europe and Africa, and the papers show that Bude tested the value of new "carriers" used by telecoms companies to judge whether they would be worth intercepting.

According to documents, dated from 2008 to 2011, a unit at Bude did this by testing samples of data to see whether surveillance targets already on GCHQ and NSA databases were making use of the new connections.

If GCHQ analysts identified a carrier they thought could be useful, they would be asked: "Can this carrier be tasked on collection system?"

Providing more permanent surveillance would often depend on whether GCHQ had suitable software and, if not, whether it was possible to upgrade systems to make it possible.

Almunia is in charge of major anti-monopoly investigations and approving mergers of companies with significant presence in the EU. He has been involved in a long-running investigation into Google over complaints about the company's alleged stranglehold on online advertising. He has also clashed with Google and Microsoft over privacy concerns and was prominent in the EU's response to the global financial crisis.

Surveillance on such a senior EU official with a major role in economic affairs is bound to alarm other European nations, and raise concerns as to whether intelligence produced from Almunia or others is shared with the US – the NSA has a number of personnel at the base in Bude and contributes millions of pounds to its budget.

Another target was the French defence and logistics giant Thales Group, which is part-owned by the French government.

In all, communications from more than 60 countries were targeted in this particular operation, with other names listed in the GCHQ documents including Mohamed Ibn Chambas, the current African Union-United Nations joint special representative for Darfur, as well as multiple African heads of state.

Imboden, from the non-profit Ideas Centre in Geneva, and Solomon Asamoah, deputy head of the Africa Finance Corporation, also appeared on GCHQ's lists.

The documents do not give any insight into why GCHQ deemed them worthy of surveillance.

In 2009, Chambas was president of Ecowas. He had been closely involved in efforts to bring peace to Liberia, and GCHQ picked up text messages he sent while in the country to receive an award.

One message read: "Thanks Kwame. Glad to know all is well. Am in Liberia for receive National Award … inde celebration." A second added: "What machine gun sounds? Am in Gbanga former HQ of Charles Taylor …"

Offices operated by the UN development programme, which administers financial relief to poor nations, and of the World Health Organisation were also among listed targets.

The targeting of German government buildings may prove the biggest political headache for the UK. The documents show GCHQ targeting German government networks in Berlin, and official communications between Germany and Georgia and Germany and Turkey. Germany's embassy in Rwanda was also a target.

The papers seen by the Guardian do not disclose the extent of any surveillance or for how long any collection took place.

However, each individual or group had a specific ID number in the agency's "target knowledge base". This indicates they had been a deliberate target of surveillance efforts, rather than accidentally caught in a dragnet.

Unlike its US counterpart, GCHQ is entitled to engage in spying relating to economic matters, but only if it is linked to national security issues.

The 1994 Intelligence and Security Act says the agency can work "in the interests of national security, with particular reference to the defence and foreign policies of Her Majesty's government; in the interests of the economic wellbeing of the United Kingdom; and in support of the prevention and the detection of serious crime". However, critics have repeatedly called for a proper definition of "national security", and raised questions about what should be permitted to protect "economic wellbeing" beyond the need to help UK companies defend themselves against the theft of intellectual property or from cyber-attacks.

Documents show GCHQ has also been keen to break into global roaming exchanges (known as GRXs), which are centres that handle routing international mobile calls to the appropriate countries and phone networks. Belgacom, which Der Spiegel revealed this year was the victim of GCHQ hacking efforts, is one such international exchange.

One 2010 presentation referring to the agency's efforts against GRXs went on to note that "diplomatic targets from all nations have an MO [modus operandi] of using smartphones" and added the agency had "exploited this use at the G20 meetings last year". The Guardian in June revealed GCHQ had engaged in extensive surveillance efforts against G20 delegates in 2009, including in order to secure advantages in trade talks and bilaterals.

On Monday, the Guardian, Der Spiegel and the New York Times jointly approached GCHQ for comment. The agency would not go into any details but said: "One of the purposes for which GCHQ may be authorised to intercept communications is where it is necessary for the purpose of safeguarding the economic wellbeing of the UK." However, the code of practice made clear this had to be "directly related to state security. Interception under this purpose is categorically not about industrial espionage."

The NSA said: "As we have previously said, we do not use our foreign intelligence capabilities to steal the trade secrets of foreign companies on behalf of – or give intelligence we collect to – US companies to enhance their international competitiveness or increase their bottom line. The United States collects foreign intelligence just as many other governments do.

"The intelligence community's efforts to understand economic systems and policies, and monitor anomalous economic activities, are critical to providing policymakers with the information they need to make informed decisions that are in the best interest of our national security. As the administration also announced several months ago, the US government is undertaking a review of our activities around the world – looking at, among other issues, how we co-ordinate with our closest allies and partners."