German government spokesman Steffen Seibert told reporters that Chancellor Angela Merkel has been personally informed of the arrest.
He declined to comment on reports by Der Spiegel magazine and the daily Sueddeutsche Zeitung that the man worked for Germany's foreign intelligence service, known by its German acronym BND.
The newspapers, which didn't identify their sources, said the man was suspected of passing on information about a German parliamentary committee investigating the activities of U.S. and other intelligence agencies in Germany. He claimed to have worked with U.S. intelligence since 2012, they reported.
Seibert said members of the parliamentary panel had also been informed of the arrest.
Reports that the National Security Agency spied on German citizens, including on Merkel's cellphone, have caused friction between Berlin and Washington since they were first published last year, based on documents leaked by former NSA contractor Edward Snowden.
Martina Renner, a member of the opposition Left Party on the parliamentary panel, said the case indicated that anyone who examined Snowden's revelations in detail was subject to scrutiny by U.S. intelligence agencies.
Her panel heard testimony Thursday from two former NSA employees, Thomas Drake and William Binney.
"If the media reports (about the case) are confirmed then there can't just be a legal response, there also has to be a political response," she said.
In his testimony, Drake claimed that cooperation between the NSA and Germany's BND greatly increased after the 9/11 terror attacks in the United States. He described the German spy agency as an "appendage" of the NSA.
Seibert said Merkel discussed "foreign policy matters" in a telephone conversation with President Barack Obama late Thursday. He said the conversation focused on Ukraine but wouldn't say whether the arrest was also discussed.
The U.S. National Security Council declined to comment Friday and BND didn't immediately return a call seeking comment.