German authorities Wednesday searched the home and office of a defence ministry employee suspected of spying for the US, media reported.
The searches were carried out in the capital Berlin, BBC quoted a federal prosecutor in Karlsruhe as saying.
This is the second such case involving the US. Earlier, an intelligence agency employee was arrested for passing secret documents to the US intelligence.
The spy case would cast a new shadow over relations between the US and Germany, which have taken a bruising since last year with the US National Security Agency (NSA) surveillance scandal sparked by revelations of fugitive US intelligence contractor Edward Snowden, the Guardian reported.
"It would be a clear contradiction of what I consider to be trusting cooperation" with the US, German Chancellor Angela Merkel was quoted as saying by the British daily Monday.
The US has promised to work to resolve the problem.
The two countries have been close allies for decades, but relations were strained last year when it was revealed that the NSA had been monitoring Merkel's phone calls.