The allegations dating back to a party at a hotel in April were first reported by the Spiegel Online news site on Monday.
Soldiers sang racist and anti-Semitic songs and one also sought to sexually assault another while he was asleep, a scene that was caught on film, the report said.
Defence Minister Annegret Kramp-Karrenbauer said the entire platoon of 30 soldiers will be withdrawn "with immediate effect".
"The misconduct of some soldiers in Lithuania is a slap in the face of all those who serve the security of our country day after day in the #Bundeswehr," she wrote on Twitter.
The platoon will return to Germany on Thursday where investigations into the allegations have been ongoing since last week, a government spokeswoman said.
Kramp-Karrenbauer said any soldiers found guilty would be "punished with the utmost severity".
Three soldiers had initially been removed from the contingent stationed in the Baltic country, according to the Spiegel report.
The German armed forces have been repeatedly rocked by allegations of right-wing extremism within their ranks.
Kramp-Karrenbauer last year ordered the partial dissolution of the KSK commando force after revelations that some of its members harboured neo-Nazi sympathies.
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