The intelligence chief was kicked out on Thursday following the revelation of two alleged spying cases within days of each other, re-igniting simmering German anger at American snooping on one of its key European allies.
"Let me emphasise the relationship between the United States and Germany is a strategic one. We have enormous political cooperation and we are great friends. And we will continue to work together," Kerry said in a joint news conference with German Foreign Minister Frank-Walter Steinmeier in Vienna.
The spying row brought back uncomfortable memories of another dispute last year when it emerged that Washington was monitoring Chancellor Angela Merkel's phone.
In the latest case, the home and office of a German defence ministry employee accused of passing secrets to the US were raided by police.
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A week earlier, a 31-year-old German BND foreign intelligence service operative was arrested on suspicion of having sold over 200 documents to the CIA.
"The thing we always have to keep in mind when we are working together is if the person across the table is possibly working for someone else at the same time, that for me isn't a trusting relationship," she told German television.
"Here we obviously have different points of view and we need to talk to one another," Merkel said, adding that she had "naturally hoped for a change" in Washington's behaviour.