Berlin police last week rejected the 13-year-old's account that she was sexually assaulted by "foreigners", but Russian Foreign Minister Sergei Lavrov yesterday lent credence to the girl's allegations and charged that her disappearance had been "hidden".
Government spokesman Steffen Seibert today hit back, saying "there is no reason, in fact it is unacceptable, for this incident to be politically exploited."
The teenager, identified by Russian media as "Liza", went missing on January 11, reportedly on her way to school.
The case sparked outrage and allegations on far-right websites and Russian media outlets of an official cover-up.
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But Berlin's prosecutors said there was no evidence that the girl was forced to have sexual relations during that period.
Martin Steltner, a spokesman for Berlin's prosecutor's office, said that it had opened an investigation against a man on possible statutory rape charges.
Sex with anyone under the age of 14, even if consensual, is a crime in Germany which is punishable by imprisonment.
"We are now working with her lawyer. He is working with her family, with our embassy," Lavrov said.
"It is clear that the girl -- absolutely for sure not voluntarily -- disappeared for 30 hours."
Lavrov said he regretted the news of Liza's disappearance had "been hidden for a very long time, for some reason."
Seibert declined to comment directly on the case.
"What I can fundamentally say is that in Germany we have a state based on the rule of law," he said.