Foreign Minister Frank-Walter Steinmeier "summoned Turkey's envoy to the foreign ministry" for talks "on latest developments in Turkey", said a ministry source.
While Ankara "has the right to counter the threat of terrorism and to deal with the bloody coup attempt through the law, that should not serve as a justification to muzzle the opposition or to put them behind bars," the source said.
Berlin felt it "could not remain silent" given the deep ties between the two countries and its people.
"It is therefore necessary to formally communicate the government's position to the Turkish government," said the source.
Both co-leaders of Turkey's Peoples' Democratic Party were detained along with nine other MPs on Friday, dramatically escalating Ankara's crackdown on leading pro-Kurdish politicians in the wake of the July 15 failed military coup.
Critics say that the arrests show that the mass raids have gone well beyond targeting the actual putsch plotters.
Relations between Ankara and Berlin have been strained in the wake of the failed coup, with Germany repeatedly expressing concern over the scope of the crackdown on suspects.
On Thursday, Turkish President Recep Tayyip Erdogan accused Germany of being one of the world's worst countries for harbouring "terrorists", saying Berlin had not responded to requests to hand over suspects from the failed coup.
After Turkish authorities on Monday detained 13 journalists from the opposition Cumhuriyet newspaper, Chancellor Angela Merkel said it was "highly alarming that freedom of the press and speech are being restricted again and again."