"The German government deliberately helped Yilmaz escape justice by placing him on a plane to Turkey," Whitaker said in a sharply-worded statement.
"The German government has refused to take any responsibility for failing to extradite him to the United States, has flouted their treaty obligations and has undermined the rule of law," the acting attorney general said.
CNN reported that US Deputy Secretary of State John Sullivan complained about the move during a "tense meeting" at the State Department on Wednesday with German Foreign Minister Heiko Maas and Germany's ambassador to the United States, Emily Haber.
A German foreign ministry source said the deportation of Yilmaz to Turkey was a "decision of the independent justice system" and was made "in compliance with the standards of the rule of law."
Relations between Germany and the United States have been strained since Donald Trump became president.
Yilmaz, a member of a group called the Islamic Jihad Union, was accused of carrying out attacks on US troops on the Pakistan-Afghanistan border in 2006.
Yilmaz also was alleged to have had contacts with the man who carried out the March 3, 2008 suicide bombing in Afghanistan that killed two US soldiers.
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