German police raided the house and the office of a man believed to be a US spy, days after an alleged double agent also said to be on the payroll of the CIA was arrested.
Federal prosecutors said security forces searched the two premises in the Berlin area on "initial suspicion of activity for an intelligence agency".
Authorities added that no arrest had been made and did not elaborate as to whom the suspect was allegedly spying for.
Local media reported the investigation concerned an employee of Germany's Ministry of Defence, possibly a German army soldier, who was collecting intelligence on behalf of the US.
Die Welt newspaper reported that the man had aroused the suspicion of Germany's military counter-intelligence agency because of his close contacts to alleged US spies.
It was the second spy case in two weeks and it threatened to sour diplomatic relations between Berlin and Washington.
Der Spiegel magazine reported that the man was an employee of the Bundesnachrichtendienstor BND ‒ Germany's equivalent of the American CIA ‒ who had, somewhat ironically, been paid by the US to provide information about a German parliamentary committee set up to investigate what kind of spying activities were being carried out by the US and other intelligence agencies in Germany.
"We have investigations in two cases of suspected espionage, a very serious suspicion," government spokesman Steffen Seibert said.
The committee was formed after allegations by NSA whistleblower Edward Snowden that the US government tapped Chancellor Angela Merkel's phone.
The US ambassador to Berlin was subsequently summoned to the Foreign Ministry.