Germany’s Defence Ministry says Ankara is blocking plans for a senior official to visit the country’s 250 personnel stationed at Incirlik air base.
As yet, there has been no official response from Turkish officials.
Six German reconnaissance jets and a refuelling plane are stationed at Incirlik.
They are part of a US-led air campaign against ISIL militants in Iraq and Syria.
Relations between Germany and Turkey have been strained recently.
The German parliament recently adopted a resolution declaring the 1915 killing of Armenians by Ottoman Turkish forces a genocide.
Ankara strongly rejects the definition.
Germany’s public broadcaster says a Turkish channel has pulled broadcasts of a children’s news programme it produces.
ZDF says Turkey’s Kanal D cited “numerous complaints” following the June 2 vote in the Bundestag.