General Keith Alexander's statement before the House Intelligence Committee came in the wake of a report in the Wall Street Journal, also on Tuesday, which cited unnamed US officials to contradict earlier accounts from French and Spanish media that alleged the NSA was scooping up millions of phone records of citizens in those countries.
The news reports had been based on leaks from former intelligence contractor Edward Snowden, who has disclosed a series of classified documents on NSA surveillance that has provoked a global firestorm.
But the NSA boss told the House Intelligence Committee that it was Spain and France who had carried out the espionage.
"This is not information about EU citizens," Alexander stressed during the hearing.
"It's about data that we and our NATO allies have obtained jointly for the protection of our countries."
Alexander said that said the media had not known "what they had in front of them" with the leaked information.
White house secretary Jay Carney, meanwhile, said only that there had been significant "cooperation" with the intelligence services of other countries.
The comments from Carney and Alexander follow on from earlier allusion by US officials to the falseness of European media reports on US spying.
The director of national intelligence, James Clapper, had said an article in Le Monde that alleged 70 million French phone calls were collected from December 2012 to January 2013 was "inaccurate" and "misleading."
But he did not specify exactly what was incorrect about the coverage.
US officials told the Wall Street Journal that the documents provided by Snowden to European media had been misinterpreted and show that phone records were first collected by French and Spanish spy agencies, and then shared with the NSA.
The officials said the document also shows that the phone records collected by the French were gathered outside of France, and then passed along to the US intelligence community.
The leaked information does not indicate that the French spied on their own citizens inside the country.
The sharing of phone data was separate from US spying on foreign leaders, including German Chancellor Angela Merkel, according to the Journal.
Both the reports on the collection of phone records and revelations of NSA eavesdropping on the leaders of friendly governments has provoked outrage among US allies.
On Tuesday, the head of Spain's intelligence agency the CNI stated: "We have always worked within the law."
But he added that the law "impeded" the agency "from commenting on relations with other security agencies".
Spain has a modern intelligence network, established partly with the assistance of George W. Bush, according to Spain's El País newspaper.
Israeli equipment was also purchased to prevent over-reliance on the US, the Spanish paper also reported on Wednesday.