In a tough-worded commentary published amid a raging bilateral row, they warned that Germany's democratic culture was at threat from the "radicalisation" of Erdogan's politics, spreading through state-backed mosques and groups.
"We must be careful Muslim communities in Germany do not fall under the sway of President Erdogan," Foreign Minister Sigmar Gabriel and Justice Minister Heiko Maas wrote.
"The slow dissolution of the separation of religion and state taking place in Turkey is poison for democracy," they said.
"Erdogan's rhetoric about enemies and his defamation of people who oppose him as 'infidels' or 'traitors' is a threat to the democratic culture of Germany."
They added: "Our country must protect the people who oppose Erdogan's cultural battle and propaganda."
Turkish EU Affairs Minister Omer Celik on Wednesday accused Gabriel of copying the "far-right and racists" in his statements in an ongoing diplomatic crisis with Turkey.
"Gabriel is not making original statements. He speaks by 'copying' from the far-right and racists," Celik wrote on Twitter in a tirade of 29 tweets criticizing Gabriel and his Austrian counterpart Sebastian Kurz, as the row between Ankara and Berlin showed no signs of slowing.
Relations between Berlin and Ankara have deteriorated sharply, particularly since a failed coup against Erdogan over a year ago and a subsequent mass crackdown on its suspected plotters.
Among the alleged state enemies and terrorist supporters behind bars in Turkey are several German or dual Turkish-German citizens, including journalists and rights workers.
Erdogan has charged that Germany is sheltering Kurdish militants, coup plotters and terrorists, but also personally attacked Gabriel in recent days.
And he has urged ethnic Turks in Germany to vote in September 24 elections against Merkel's conservatives and their coalition partners the Social Democrats, the party of Gabriel and Maas.
The escalating tensions have split the Turkish community in Europe's top economy, the largest diaspora abroad, which is a legacy of Germany's "guest worker" programme of the 1960s and 70s.
The two ministers warned in their Spiegel Online commentary that Erdogan's "dangerous ideologies must not be imported to Germany via certain mosques."