German budget airline Greenwings said the alert had been triggered when a man who appeared to be mentally unstable had threatened an attack on one of its planes.
Stockholm police said a suspect had been taken into custody and would undergo psychiatric evaluation.
"The plane has been moved from the gate and will be examined by technicians," the police said in a statement, without giving further details about the company involved.
"It's not the first time we've received this kind of threat but it is not very common," police spokesman Lars Bystroem told AFP.
Greenwings said in a statement to the Dagens Nyheter newspaper that an incident on board their plane bound for Hamburg had triggered the police operation.
"A man who appeared mentally unstable threatened an attack. As a result the police were contacted and the 49 passengers were asked to leave the plane. The man is now in the hands of the police," it said.