White House press secretary Josh Earnest wouldn't comment on Germany's decision but said the US takes intelligence matters "very seriously."
"I don't want you to come away from this exchange thinking we take this matter lightly," he said, adding that the US and Germany continue to have a strong partnership.
The reports last year that the National Security Agency had targeted Merkel and Internet traffic have triggered a German criminal investigation and a parliamentary probe.
On Wednesday, German police raided properties in the Berlin area in what Seibert said was a case involving "a very serious suspicion" of espionage.
German media reported that the man being investigated worked at Germany's Defense Ministry in a department dealing with international security policy, and he had aroused suspicion because of his close contacts to alleged US spies.
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 CIA.
German Foreign Minister Frank-Walter Steinmeier said he could not comprehend why the US 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.
Interior Minister Thomas de Maiziere said the political fallout appeared to outweigh any harm done to Germany by the alleged spying.
"If the situation remains what we know now, the information reaped by this suspected espionage is laughable," de Maiziere said in a statement. "However, the political damage is already disproportionate and serious."
Under the elaborate rules of international diplomacy, Germany's move to kick out the spy chief was a request two steps short of a formal expulsion.
In the past two years, Germany has also asked diplomats from Syria and Pakistan to leave the country.
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