Lufthansa had to cancel 33 European flights, and services across its global network were delayed, following a computer fault in its check-in system on Thursday, the airline said.
The company's Star Alliance partners, Britain's bmi, Poland's LOT and Austrian Airlines were also affected by the problem with the Unisys computer system, Star said.
The flight cancellations affected about 3,000 passengers, while short-haul and long-haul departures were delayed by up to two hours, Lufthansa said. Some freight normally carried by plane had to be transported by truck.
Lufthansa said the check-in system was up and running again by 1030 GMT, but added that delays were continuing. The airline said it hoped services would return to normal on Thursday.
"Lufthansa regrets the inconvenience caused to passengers," the airline said. "The (services) should go back to normal again during the course of the day."
At Berlin's Tegel Airport there were delays as check-in staff had to hand-write tickets and tell passengers there was no assigned seating. At Munich Airport people were scrambling for seats, with elderly people being pushed aside as they tried to get to the front of the queue.
A Lufthansa check-in agent said the problem was not caused by a virus but by the launch of a new computer program overnight which brought the system down.
A spokeswoman for bmi, which uses the same check-in computer system, said the airline's network also suffered delays, though bmi had not canceled any flights. An Austrian Airlines spokesman said it too had no cancellations, although there were some delays.
The problem also affected Lufthansa's regional airlines, including Eurowings and Air Dolomiti.
Unisys said it deeply regretted the failure of its check-in system, which went down following a planned outage.
"After being rebooted, the operating system and hardware ran smoothly for approximately 90 minutes until a software problem brought the check-in system application down," Unisys said. The company had to install a software change to fix it.
