Von der Leyen told the Welt am Sonntag newspaper that any proof of wrongdoing could result in serious consequences for the temporary employment agency used by Amazon.
"There is a strong suspicion here which is why we need to lay all the facts on the table," she said. "If the investigation shows there is something to the accusations against the temporary placement agency then its licence is at risk."
A public television documentary broadcast Wednesday said workers brought in from crisis-hit countries such as Spain to help at Amazon warehouses faced bullying from security personnel, some of whom wore clothing associated with neo-Nazi groups.
It added that Amazon paid the workers less than advertised and that their belongings were regularly searched in the temporary housing they were provided.
Services union Verdi has long accused Amazon of paying its seasonal workers unfair wages and going overboard on surveillance.
The US company, which has about 7,700 people on staff in Germany and hires additional temporary workers at peak times, said it was looking into the allegations and would not tolerate intimidation at its sites.
Hensel European Security Services, the company targeted in the documentary, also denied any wrongdoing.
"The accusation that our company harbours far-right views or supports them is false," it said in a statement.
It confirmed that its staff had searched temporary workers' rooms but said this had taken place with the agreement of the hotel and in order to investigate reported theft.