Foreign ministry spokesman Martin Schaefer told reporters it had "specific indications" that the two Germans, a married couple, had been taken into police custody over the weekend.
It is not known what the pair were arrested for, but Schaefer added one has apparently been released and told to leave Turkey.
"That means the nightmare of so many German nationals who wanted nothing else than to have a holiday in Turkey continues," he said.
"It can affect anyone who decides to travel to Turkey. You expect no danger and suddenly you're in a Turkish prison - that is the sad reality we are confronted with."
Schaefer said that in the face of such "capriciousness" by the Turkish authorities, Germany would have to consider putting Turkey on its travel blacklist in future.
"If it becomes daily routine for the Turkish authorities to detain German citizens at the border and put them in police custody... then it is possible that the moment will have arrived that a travel advisory will be issued," he said.
"Then Turkey would join a list of countries such as Libya, Yemen and Syria in which no one would think of going on holiday."
Ties between Berlin and Ankara have soured since last year's attempted overthrow of President Recep Tayyip Erdogan and Germany's strong criticism of an ensuing crackdown in Turkey which has seen more than 50,000 people arrested.
Relations further deteriorated after the detention of several German citizens including Deniz Yucel, a correspondent for Die Welt newspaper.
Eleven Germans are currently held by Turkey for political reasons, including three who have been detained since the summer of 2016, according to the German foreign ministry.
Germany had updated foreign ministry travel advice in July to warn citizens that they could face arrest if they travel to Turkey.
In a tit-for-tat update to its own travel guidance, Turkey on Saturday warned citizens living in or travelling to Germany "to be cautious, taking into account the situation in Germany where they could risk xenophobic or racist treatment".
Chancellor Angela Merkel, campaigning for a September 24th general election, dismissed the advisory, saying Germany stood for "freedom of speech and the rule of law".
Merkel has also announced her intention to speak with her EU counterparts to call off membership talks with Turkey.