Thomas Cook's German subsidiary has filed for for insolvency, according to the German Press Agency.
Condor asked the German Government for a bridging loan on Monday, as unions and officials scrambled to keep the airline flying and staff in jobs.
"I assure you that we will do everything in our power and leave no stone unturned, so that our fleet continues to bring our guests reliably to their holiday destinations all over the world and back home as usual," Ralf Teckentrup, chairman of Condor, said.
On Tuesday, the German government said it would guarantee a €380 million bridging loan to keep it operating.
It now seems that hasn't been enough to keep the airline solvent after its parent firm's liquidation.
Condor employs around 4,500 people.
News also broke on Wednesday that Thomas Cook's Polish unit, Neckermann Polska, has also announced that it is insolvent.
Neckermann Polska, said on Tuesday that it has cancelled some flights and temporarily stopped taking any new bookings, citing the impact of its parent company's collapse on the global tourist industry.
On Monday the company said it was continuing day-to-day operations and that its financial condition was stable.
Some flights operated by Thomas Cook's Nordic business have also been cancelled or delayed as the subsidiary battles to survive the collapse of its parent company earlier this week.
