Lufthansa scrapped hundreds of flights at its CityLine and Eurowings regional carriers on Monday as pilots walked out in a 24 hour strike over pay.
Lufthansa said 202 services were cancelled up until 1100 GMT. Further flights could be cut later in the day, a spokesman for the carrier said.
The strike hit passengers at airports across Germany, including Lufthansa's main hubs at Frankfurt and Munich.
The walkout started at 2200 GMT on Sunday and followed a breakdown in talks between the Vereinigung Cockpit pilots' union and the airline and a vote for strike action by pilots.
In a separate dispute over pay for ground staff and cabin crew at Lufthansa, talks are due to resume between the carrier and the Verdi union on Wednesday after they failed to reach a deal this week.
