An Amazon spokeswoman said it had ensured that "the criticized security service is not used any longer, effective immediately," a day after a German government minister called for a probe.
A public television documentary broadcast last week alleged that 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.
"As a responsible employer of approximately 8,000 salaried logistics employees, Amazon has zero tolerance for discrimination and intimidation and expects the same from every company we work with," Ulrike Stöcker, spokeswoman for Amazon's German branch said in a statement.
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.
Labour Minister Ursula von der Leyen told Sunday's Welt am Sonntag newspaper that any proof of wrongdoing could result in serious consequences for the temporary employment agency used by Amazon.
"If the investigation shows there is something to the accusations against the temporary placement agency then its licence is at risk," she said.