Unicef and Medecins du Monde were among the organisations listed in the latest batch of secret documents leaked by fugitive Edward Snowden to be published by a newspaper.
It said the papers revealed that British listening post GCHQ had Joaquin Almunia, vice- president of the European Commission with responsibility for competition policy, in its sights.
The revelation appears to have strained diplomatic relations, prompting an angry response from the European Commission, which issued a statement saying the claims "deserve our strongest condemnation" if proved true.
"This is not the type of behaviour that we expect from strategic partners, let alone from our own member states," it said.
Among documents dating back to January 2009 is an email address listed as belonging to the "Israeli prime minister", then Ehud Olmert. Also being targeted was an account understood to have been used to send messages between the then Israeli defence minister, Ehud Barak, and his chief of staff, Yoni Koren.
Other targets include the UN development programme and German government building, according to The Guardian.