The European Union will discuss "data protection and privacy rights" alongside trade talks with the United States next week.
But the head of the 28-nation bloc's executive commission, Jose Manuel Barroso, said broader concerns about US intelligence activities would have to be raised by member states individually because they fall under the category of national security.
Reports last weekend that the US National Security Agency bugged EU diplomatic offices in Washington and infiltrated its computer network angered European officials and many leaders called for the NSA's surveillance activities to be discussed in parallel with trade talks opening next week in Washington.
Lithuania, which holds the rotating EU presidency, said the process would start with a meeting on Monday. "It will deal with data protection and privacy rights of EU citizens falling within the competence of the EU, addressing the scope and composition of future meetings," the presidency said.
Obama administration participants in the meeting will include officials from the Department of Justice and from the Office of the Director of National Intelligence, a Justice Department spokesman said.
Mr Barroso said that process was "very important to build and to enforce the confidence that is necessary also to pursue very ambitious agreements that we hope to conclude with the United States namely, in the field of trade and investment".
However, he added that "intelligence matters, those that are a matter of national security, not (falling under the purview) of the European Union, will be discussed by the member states with the United States".
The EU chief was speaking in Vilnius, the capital of Lithuania, which has taken over the six-month rotating presidency of the 28-member bloc as transatlantic relations have been overshadowed by claims of US eavesdropping.
EU home commissioner Cecilia Malmstrom suggested that two flagship information-sharing accords with the US could be suspended due to the issue. In a letter to US Homeland Security chief Janet Napolitano and Treasury under secretary David Cohen, seen by The Associated Press, Ms Malmstrom said that "mutual trust and confidence have been seriously eroded".
The bad blood could take a toll on the Passenger Name Record programme, in which Europe provides the US with airline passenger information, and the Terrorist Financing Tracking Programme. Both accords followed the September 11 2001, terror attacks in the US.