Turkey has reacted with fury to the documents, disclosed by German public broadcaster ARD, with the Turkish foreign ministry quipping that the claims reflect a "twisted mentality" in Germany.
ARD said the report was supposed to be confidential and commissioned by the Interior Ministry after a parliamentary request from the leftist Linke party.
It claims that "as a result of the increasing Islamization of Ankara's domestic and foreign policy since 2011," Turkey has links to Hamas in Gaza, the Muslim Brotherhood in Egypt and groups of armed Islamist opposition in Syria.
Turkey's foreign ministry issued a statement calling the allegations further "evidence of the biased attitude that, for some time now, attempts to demoralise our country while taking aim at our president and government."
According to a report by German Intelligence officials, 25% of #ISIS sympathizers in #Germany are #Turkish origin". #Erdogan #IslamicState
— Hamseda (ن) (@HamsedaCA) August 17, 2016
It insisted that Turkey was a country that "always fights terror sincerely regardless of the origin."
German Interior Minister Thomas de Maiziere has defended the report, telling the German regional broadcaster RBB:
"There's nothing to regret."
He said the report showed one aspect of Turkey but that there were other factors influencing relations.
This secret report is embarrassing for chancellor Angela Merkel, who has built a policy of friendship with Erdogan. https://t.co/mku7xaYYaF
— نMare Kranjc™ (@Max970) August 18, 2016
However, the German government on Thursday (August 18), was at pains to emphasize the ongoing working relationship between Germany and Turkey.
Political commentators say the incident has highlighted the divisions within German Chancellor Angela Merkel's government.
There are also serious concerns across Europe about the strength of a landmark EU-Turkey deal, brokered by Germany, to try and stem the flow of migrants to Europe.
Turkish President Recep Tayyip Erdoğan has threatened to abandon the pact if the EU does not grant Turkey's demand of visa-free travel for Turkish citizens within the bloc.
"If that is not what will happen… no decision and no law in the framework of the readmission agreement will come out of the parliament of the Turkish republic," Erdogan said.
This week's embarrassing revelations are unlikely to help with the ongoing negotiations over the migration crisis. They are also the latest in a catalogue of blows to an already stony Germany-Turkey relationship this year.
In May, a German comedian's poem about President Erdogan sparked a diplomatic row. Jan Böhmermann accused Erdogan of "repressing minorities, kicking Kurds and slapping Christians while watching child porn."
A furious Erdogan demanded that the satirist be prosecuted. Chancellor Merkel capitulated, and faced heavy criticism in Germany for agreeing to the Turkish President's demands.
A month later, German legislators voted to call the massacre of Armenians in 1915 a "genocide". Turkey admits that there were mass killings but fiercely contests that the slaughter was part of a genocidal campaign of ethnic cleansing. A spokesman for Turkey's ruling AKP party rejected the vote, saying it had "seriously damaged" relations.
Then, following the July 15 failed coup attempt in Turkey, relations soured further.
EXCLUSIVE: Ankara didn’t recognize threat posed by #Gulen — @MevlutCavusoglu https://t.co/QeuLrOZEnu #TurkeyCoup pic.twitter.com/o7YYHwcUhx
— Sputnik (@SputnikInt) August 18, 2016
There is huge concern across the West, at what is increasingly being seen as an authoritarian crackdown on dissenters by President Erdogan. Tens of thousands of troops, police, judges and civil servants have been detained or dismissed in a massive purge, with some Erdogan supporters now calling for the death penalty to be reinstated to punish the coup-plotters.
Without addressing this week's leaked documents, German Government spokesman Steffen Seibert, said Berlin still viewed Ankara as a vital partner in the ongoing fight against Islamic State, a conflict that has spilled over the border into Turkey itself.
