Beyond Turkey's strategic importance, von der Leyen warned that rupturing ties could give the democratic Turkish opposition to President Recep Tayyip Erdogan the sense the West was leaving it in the lurch.
"Turkey is not making it easy for us within NATO. But no one should believe that a Turkey outside NATO would listen better to us or would be easier to deal with than a Turkey in NATO," she told AFP.
Von der Leyen, who has served as Chancellor Angela Merkel's defence chief since 2013, said that NATO provided a platform for the West to "discuss - sometimes heatedly - our convictions about democracy and open society".
"We must not abandon the many Turks who don't want an expansion of the president's powers with the upcoming referendum," she said.
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Ankara is locked in a dispute with several European countries which have sought to stop Turkish ministers from holding rallies on their soil ahead of the April referendum on expanding Erdogan's powers, leading the Turkish leader to rail against "Nazi practices".
German Interior Minister Thomas de Maiziere yesterday said Ankara was playing the victim with its broadsides against NATO allies to galvanise support ahead of the referendum.
Von der Leyen rejected the call, saying the soldiers were not in Incirlik to protect Turkey but as part of the international coalition against the Islamic State group "which is entering a decisive phase in Raqa and Mosul".
"It would weaken us and would not be a smart decision".
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