“Discussions with investors and partners have shown that the German unit…has a chance of a future,” the company said in a statement.
But it was “forced to file for bankruptcy with the effect of detaching it from the complex financial linkages and liabilities” of the parent company, it added.
Thomas Cook's German subsidiary employs around 2,000 people, service sector union Verdi said.
The worker representatives added that it was a “harsh blow for workers and their families”, despite the fact that the company had been “well run” in Germany.
“Everything must now be done to make continued operations possible and preserve jobs,” Verdi added.
“The aim of the restructuring is to continue the profitable business of the German operator, which was for a long time burdened by the weak performance of Thomas Cook in Britain, and Brexit,” the company said.
German customers presently on holidays booked through Thomas Cook will be covered by Thomas Cook's insurer Zurich Insurance, the DRV tour operators' association said.
As of Monday, there were about 140,000 German tourists abroad through the travel operator. Thomas Cook said that a further 21,000 people in German who were slated to fly on Monday and Tuesday must now stay at home.
The German branch's bid to keep going matches a move by the French division on Tuesday.
Meanwhile, the Austrian unit said Wednesday it was also planning to file
for bankruptcy “in the course of the day”.
Separately, Berlin has granted Thomas Cook group's profitable German airline Condor a loan of €380 million to continue flying, as it seeks to chart its own course separately from the parent company.