The action is being held in four sites across the country in a bid to allow a collective bargaining agreement for better pay and conditions.
"Collective agreements are a sign of respect and recognition of work," said Verdi board member Stefanie Nutzenberger.
The powerful union Verdi called on staff at the largest German warehouse in Bad Hersfeld, eastern Hesse, in Rheinberg and Werne, both in North Rhine-Westphalia, and in Koblenz, Rhineland-Palatinate, to down their tools on Monday.
The industrial action in Rheinberg and Werne is expected to last until the end of the day on Thursday. In Bad Hersfeld the strike will last until the end of Tuesday, and in Koblenz it will be limited to Monday, reported German media
Verdi has long been calling on Amazon to change its rules to allow a legally binding collective bargaining agreement for the company's employees, which it believes would lead to better pay and working conditions. The union is seeking an agreement similar to that available for retail workers and other mail order companies.
However, Amazon has previously said that its workers already earn a higher wage than the industry average. Employees start with a salary of at least €10.78 per hour. The firm sees itself as part of the logistics industry rather than a retail and mail order company.
Throughout Germany, Amazon has 12 warehouses at 11 locations and, according to its own figures, employs around 13,000 permanent staff.
Amazon said the strikes would not affect deliveries because the majority of staff had come to work.
The e-commerce giant has emphasized that it it is possible to be a fair and responsible employer without a collective agreement. The dispute has been ongoing since 2013.
The union has warned that further strikes could take place, including over the Easter period.