The daily Sueddeutsche Zeitung reported, without naming sources, that the man being investigated worked at Germany's Defense Ministry and is suspected of spying for the U.S. News website Spiegel Online reported, also without naming sources, that the man worked in a department dealing with international security policy and had aroused the suspicion of Germany's military counter-intelligence agency because of his close contacts to alleged U.S. spies.
Defense Ministry spokesman Lt. Col. Uwe Roth declined to confirm the reports, but said the case fell "into the ministry's area of responsibility" and that Defense Minister Ursula von der Leyen had been informed.
State Department officials traveling with U.S. Secretary of State John Kerry in Beijing had no immediate comment.
Last week, a 31-year-old German intelligence employee was arrested on suspicion of spying for foreign powers since 2012. German media have reported that he spied for the United States and came to authorities' attention when he recently offered his services to Russian officials in Germany by email.
The case has frayed relations between Berlin and Washington, which were already strained by reports last year that the National Security Agency had targeted Chancellor Angela Merkel's cellphone and conducted mass surveillance of Internet traffic in Germany. Those allegations have resulted in a criminal investigation and the creation of a parliamentary panel tasked with probing the NSA's activities in Germany.
The U.S. ambassador to Berlin was summoned to the Foreign Ministry on Friday after news of the first case broke.
Ambassador John B. Emerson was at the ministry again Wednesday for a meeting with a senior official, Foreign Ministry spokesman Martin Schaefer said. U.S. Embassy spokesman Peter Claussen said the meeting had been arranged on Tuesday at the embassy's request.
German Foreign Minister Frank-Walter Steinmeier said he was at a loss to understand why the U.S. would spy on his country.
"We speak to each other all the time, and nobody keeps their views secret," he said in an interview published Wednesday by the Saarbruecker Zeitung. "The attempt to use conspiratorial methods to find out about Germany's position isn't just unseemly, it's unnecessary."
Lora Anne Viola, an assistant professor in American foreign policy at Berlin's John F. Kennedy Institute, said the spy cases appeared to mark a low in U.S.-German relations.
"I think it's going to be difficult to repair this with words alone," she said, adding that it was in Washington's interest to reach out to Germany.
"Without partners, without Germany, it's very difficult for the U.S. to act on the foreign stage," Viola said. She cited the case of Ukraine, where Germany has played a key role reaching out to Russia while also rallying European countries around the idea of sanctions.
Erich Schmidt-Eenboom, an expert on Germany's intelligence agencies, said the reaction in Berlin would likely have been muted at any other time. "They would have resolved this the way they've done since the 1950s, which is switch off the German spy and send his American handler home."
"But the NSA scandal is forcing the German government's hand," he said. "It's been trying for months to play down the scandal so this new case has blindsided them."
Schmidt-Eenboom said cooperation between the American and German intelligence agencies — particularly the CIA and its German counterpart the BND — was traditionally good.