French President Francois Hollande has laid down the law to Barack Obama, telling him that spying on the EU must "immediately stop".
Angela Merkel, the German Chancellor, also weighed in, with a spokesman saying: "Bugging friends is unacceptable".
Both countries warned that relations with the United States could suffer as a result.
On Sunday, German magazine Der Spiegel claimed the National Security Agency placed bugs inside the EU offices in Washington and infiltrated its computer network.
The tactics were condemned by European Parliament chief Martin Schulz, who said he was "deeply worried and shocked".
According to Der Speigel, a 'top secret' document sets out "how the secret service attacked the EU's diplomatic representation in Washington."
Bugs were installed in the office, it said, claiming: "Americans were able to access discussions in EU rooms as well as emails and internal documents on computers."
France, Germany and Greece were all seen as "targets," according to the documents.
On Monday, US Secretary of State John Kerry said it was "not unusual" for countries to protect their national security interests, the BBC reported.
"Every country in the world that is engaged in international affairs of national security undertakes lots of activities to protect its national security," he said.
Fugitive ex-CIA analyst Edward Snowden, who leaked the documents, is holed up at Moscow airport as the United States tries to extradite him for espionage.