Karstadt announced on Friday that its stores in Hamburg Billstedt, Stuttgart, Göttingen and Cologne will shut on June 30th 2015.
Its outlet in Frankfurt Oder will close on April 30th 2015 and the Paderborn shop on September 30th of that year.
New chief executive Stephan Fanderl said: "The redevelopment will require a lot from us. Without some very painful decisions, as well as branch closures we can not ensure the survival of the company."
President of the board, Wolfram Keil, added: "We are only at the beginning of a long process. Karstadt is facing a profound and comprehensive change.
"With the right approach, with the newly established management team and with the support of our employees, we can turn it around."
But union Verdi, which represents Karstadt workers, will not take the restructure lying down. Stefanie Nutzenberger from Verdi said it was a "bitter day" for employees.
The 17,000 staff are also being asked to make financial sacrifices. Fanderl suggested on Friday that Christmas bonuses may not be paid this year.
He also suggested to business daily Handelsblatt that there were question marks over the future of another eight to ten stores.
Karstadt was declared insolvent in 2009 and was in the red in the 2013/14 financial year. In lost around €130 million in 2013.