Pilots and cabin crew reportedly refused to fly over fears that the crash may be linked to a repair to the nose-wheel landing doors, according to an unconfirmed report in Spiegel magazine.
It emerged that Germanwings A320 which crashed in the French Alps had been grounded for an hour for repairs the day before the air disaster.
Lufthansa has denied any link between the repair and the cancelled flights.
The airline confirmed that the aircraft had been grounded for an hour on Monday for repairs to the nose-wheel landing doors, but insisted the issue was not "safety-related".
"The repair was purely to fix a noise that the door was making, and the aircraft was flying again from 10am on Monday," the spokesman said.
It completed several flights safely after the repair before the accident, they added.
The airline spokesman said the crews refused to fly for "personal reasons". They later admitted that several Germanwings flights had to be cancelled after crews refused to fly, but said it was because they were in "deep distress" over the accident.
More disruption is expected on Wednesday after Germanwings flights from Dusseldorf to various destinations were cancelled. Three flights from Stuttgart were also cancelled.
As passengers waited to board planes at the gates, there were reports of airline ground staff advising travellers to hire cars to get to their destinations.
Passengers waiting for news described communication with the airline as "chaotic" and "poorly coordinated."
Sven Becker, editor of German newspaper Spiegel, reported seeing long queues at information desks, with flights to Madrid, Stockholm and London also cancelled.