A spokeswoman for Germanwings' parent company, German flag carrier Lufthansa, said that "Lufthansa flights are going ahead as planned. One Germanwings flight has been cancelled because pilots don't feel they are in a position to fly."
She declined to say how many pilots declined to work today.
The flight cancelled was the connection from the western German city of Duesseldorf to Barcelona. The Airbus that crashed yesterday killing all 144 passengers and six crew was travelling to Duesseldorf from Barcelona.
"It has nothing to do with safety. The pilots have friends and colleagues who have died," Handwerg said on public television.
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"That is such a heavy emotional burden that it's better not to get into the cockpit."
Already yesterday, Germanwings had reported "occasional flight disruptions within its route network" as pilots were too shocked to fly following the news of the crash of an A320 Germanwings jet.
It was the first fatal accident in the history of Germanwings, and the deadliest on the French mainland since 1974.