German police say a suspect package containing a clock, detonator and batteries was found on a Munich-bound plane.
The suspicious parcel was detected in Namibia before being put on the flight.
The scare follows yesterdays move by German authorities to boost security checks at transport hubs and other busy areas.
Germany’s government said the extra measures were taken after receiving intelligence of a planned terrorist attack by Islamic extremists.
At one of Berlin’s main railway stations, most commuters seemed unconcerned.
One man said: ‘‘I did read about it this morning, and can say I’m only slightly disturbed. At the moment I don’t think I’ll change any of my behaviour.’‘
‘‘One should avoid big gatherings I think, and apart from that I think everything will be normal,’‘ said another man.
Earlier in the capital, German police announced a bomb disposal team had destroyed a suitcase in Berlin’s Schoeneberg district, but said later that it did not contain a dangerous device.
Germany has almost 5000 troops in Afghanistan, but up until now has escaped a major attack like the Madrid and London bombings.