"There are accusations from election observers, from Russian opposition members who speak of massive irregularities," the spokesman, Steffen Seibert, told reporters in Berlin.
"These must be taken seriously and should be clarified," he added.
Russia's opposition accused the authorities of mass voter fraud as election results on Monday showed the ruling United Russia party winning a sweeping majority in parliament.
The three-day vote that ended on Sunday followed an unprecedented crackdown on critics of President Vladimir Putin and came with pre-election polls showing United Russia's popularity at a historic low.
But the party still claimed a two-thirds majority in the lower house State Duma, with United Russia's Andrei Turchak saying it was a "convincing and clean victory".
Ties between Berlin and Moscow have grown increasingly fraught in recent months over alleged espionage cases, the poisoning and jailing of Kremlin critic Alexei Navalny as well as repeated cyberattacks against Western allies.
The West has accused the Russian government of poisoning Navalny with the Soviet-era nerve agent Novichok in August 2020, which the Kremlin denies.
Navalny was treated in Berlin before returning to Moscow several months later. Upon landing at the airport, he was imprisoned, sparking demands from the West for his release.
To add to the tensions, the German government earlier this month accused Russian hackers of cyber attacks against lawmakers in the run-up to Germany's elections on September 26.