Obama will speak directly to German Chancellor Angela Merkel about the PRISM program that was revealed in newspaper articles last week, and point out it is purely aimed at thwarting terror attacks, a senior aide said.
"We understand the significant German interest in privacy and civil liberties," said Ben Rhodes, a US deputy national security advisor, adding that Obama would point out legal and political safeguards around the program.
"I think our point is that this is focused very specifically on one goal, which is, you know, how do we disrupt terrorist activity, how do we mitigate security threats, both to us and to Germany," he said.
Rhodes also noted that Germany had served as a "staging" area for some of the hijackers who plotted the September 11 attacks in 2001.
The German government said earlier in the week it was sending a list of questions to the Obama administration about the program.
Under the scheme, the US National Security Agency can issue directives to internet firms like Google or Facebook to gain access to emails, online chats, pictures, files and videos uploaded by foreign users.
The European Union has also expressed disquiet over the program and warned of "grave adverse consequences" to the rights of European citizens.
Germany had earlier Friday signaled disappointment that a meeting with US Internet companies Microsoft and Google over the PRISM program had not yielded sufficient answers.
Merkel's spokesman has said the issue will arise during Obama's visit to Berlin next week.
Obama is due to arrive in Germany on Tuesday, on a visit that will see him give a speech at the Brandenburg Gate and hold talks with Merkel.