The Istanbul-bound flight TK1672 was already taxiing for takeoff on the runway of Cologne-Bonn airport when it was stopped and its 111 passengers bused back to a terminal.
The threatening phone call received around 0815 GMT referred to the flight and was considered sufficiently credible by federal police to launch the security operation.
A sniffer dog then initially responded to a piece of hand luggage, but federal bomb disposal experts at 1140 GMT gave the all-clear.