Berlin attempted on Wednesday to head off the renewed tensions with Turkey after Ankara lashed out at a confidential German government document accusing the nation of promoting radical Islamic groups.
"We consider Turkey to be partner in the fight against Islamic State," Chancellor Angela Merkel’s spokesman Steffen Seibert said.
However, Ankara demanded that Merkel's government clarify the contents of the confidential document drawn up by the Interior Ministry in Berlin, which referred to Turkey as a "central platform" for Islamist groupings. The report was leaked to the German press.
Tensions between Berlin and Ankara have been building for months. Relations hit a low point in June when the German Parliament declared that the killings a century ago of as many as 1.5 million Armenians at the hands of the Ottoman Empire, the successor state to modern Turkey, was genocide.
Then last month Ankara was angered when Germany's top court banned Turkish President Recep Tayyip Erdogan from addressing via a live video link a Cologne rally to show support for Turkey's leadership after last month's failed military coup.
Ankara responded to the constitutional court's ruling by threatening to tear up the EU's refugee deal with Turkey, which is the cornerstone of Merkel's plan to stem the flow of asylum seekers into Germany.
However, Seibert insisted that Berlin saw no reason "to place this significant [refugee] agreement into question" after public broadcaster ARD published extensive excerpts from the confidential document.
The allegations set out in the Interior Ministry document are further "evidence of the biased attitude that, for some time now, attempts to demoralize our country while taking aim at our president and government," Turkey's Foreign Ministry said.
The ministry also said "certain political circles" were obviously behind the claims.
A German envoy in Ankara has already held talks with Turkish officials following the publication of the document, which emerged from a parliamentary question lodged by the opposition hard-left Die Linke Party.
A spokesman for the German Interior Ministry said the nation's intelligence services were "not naive" when it came to issues surrounding Turkey, which like Germany is a member of the NATO military alliance.
But he said officials had erred in not including the Foreign Ministry when preparing the answer to the parliamentary question.
The Interior Ministry document claimed: "As a result of the increasing Islamization of Ankara's domestic and foreign policy since 2011, Turkey has become a central platform for action for Islamist groupings in the ... Middle East region."
It also accused Erdogan and his ruling Justice and Development Party of providing support to the Muslim Brotherhood in Egypt, Islamist opposition in Syria and the radical Palestinian group, Hamas.
However, the Foreign Ministry in Ankara hit back saying Turkey is a country that "always fights terror sincerely regardless of the origin." the statement said.