The online retailer has vowed to launch an investigation after the allegations were made in a documentary aired on German television station ARD.
In the film, alleged temporary Amazon workers claimed to have been subjected to constant searches of living quarters and kitchens, paid less than promised and intimidated by guards wearing Thor Steinar clothing.
The Thor Steinar brand is strongly associated with Germany's neo-Nazi scene and has been banned at football matches in the territory for this reason.
ARD further claims that the security firm at the centre of the scandal, HESS Security, was named after Adolf Hitler's deputy Rudolf Hess, and accused its head of having links to football hooliganism.
Amazon has issued a statement distancing itself from HESS Security, claiming it did not hire the firm directly and vowing to investigate the complaints.
"The security firm was not contracted by Amazon. We are, of course, currently examining the allegations concerning the behaviour of security guards and will take the appropriate measures immediately," a spokesman said. "We do not tolerate discrimination or intimidation."
Amazon employs around 7,700 staff at seven distribution centres in Germany but brings in thousands more to fulfil the increased demand over the Christmas period.