The official is said to have acted as a CIA contact at the US embassy, reports say, in a scandal that has infuriated German politicians.
A 31-year-old German intelligence official was arrested last week on suspicion of spying.
Reports on Wednesday said an inquiry had also begun into a German soldier.
“The representative of the US intelligence services at the embassy of the United States of America has been told to leave Germany,” government spokesman Steffen Seibert said.
The chairman of the Bundestag (German parliament) committee overseeing the German secret service said the action was taken because of American spying on German politicians and its failure to co-operate and provide adequate responses.
The US has not denied allegations that a German intelligence agency employee arrested last week was passing secret documents to the US National Security Agency (NSA).
However, the latest reports that a soldier within the defense ministry was also spying for the US were considered more serious. Although no arrest was made, searches were carried out on Wednesday at the ministry and elsewhere.
The US and Germany have been close allies for decades but relations were hit last year when it emerged that Chancellor Angela Merkel’s mobile phone had been monitored by the NSA.
On Thursday, Angela Merkel said spying on allies was a “waste of energy”.
“We have so many problems, we should focus on the important things,” she said at a news conference with visiting Moldovan PM Iurie Leanca.
Angela Merkel has tried to maintain a balance between condemning the US actions but also maintaining cordial relations. However, each revelation has made that balance harder to achieve, he adds.
The scale of the US agency’s surveillance was revealed by former NSA contractor Edward Snowden, who fled the US and is now a fugitive in Russia.
The German intelligence official arrested last week was alleged to have been trying to gather details about a German parliamentary committee investigating the NSA spying scandal.
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