Official proceedings began after the firm's management made a complaint to the authorities, a spokesman for the state prosecutor said on Wednesday.
Caro Lobig, reporter for German TV channel RTL, had worked for three months at Zalando's logistics centre in Erfurt (under the alias Julia) to produce the insider account that revealed harsh working conditions.
The exclusive report in the magazine programme "Extra" accused the company of contravening workers' rights and forcing employees to work to the limit of their physical capacity.
Zalando rejects the allegations and submitted the complaint about RTL's conduct on the grounds that secret footage Lobig had taken inside the Erfurt plant had been broadcast before the firm was allowed to comment on the material.
But a spokesman for RTL said they were relaxed in the face of legal action by Zalando and would continue reporting about the firm's conduct.
Lobig worked in the "Picktower", the giant storage unit in Zalando's logistics warehouse, collecting products for delivery.
She reported that according to a pedometer she smuggled in, she was walking between 18 and 27 kilometres every day.
The RTL report alleged employees were constantly monitored, sitting down was "not looked kindly upon" and quoted an insider as saying "anyone who becomes inconvenient gets disposed of".
But Zalando boss David Schröder said in a statement on Tuesday that the programme's portrayal of their company was misleading.
"In our view the depiction in the report in no way shows the workplace culture and the atmosphere among employees in our logistics centres."
He highlighted that external employee questionnaires and evaluations of working conditions at Zalando had yielded positive results, claiming 88 percent of their Erfurt employees told a survey in October 2013 that their work was "fun".
Schröder also denied claims they had "covered up" the death of an employee from overwork at the Erfurt centre and underlined that Zalando employees are offered "a suitable salary, positive work environment and possibility of advancement".
"As a company and a team we have stood from the beginning as a unique success story," he said.
"We are going to stay the course, together with our colleagues."
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