Posting on Stay Safe, the Facebook page run by BAZL, an administrator for a pilots group said the “newest attraction” in the cockpit was Pokémon hunting.
“This should not be allowed as it is distracting,” said Rita Keller.
Responding, BAZL said “There is no legal basis for Pokémon, at least not in aviation law.”
“We appeal to your common sense! Fly safely and capture your Pokémon on the ground.”
One commenter added: “It's tragic this has to be spelled out”.
The world's newest gaming craze, Pokémon Go was made available in Switzerland on Saturday and can now be played in some 40 countries around the world.
The augmented reality game by a Californian company is a mobile phone app in which users can hunt and capture creatures called Pokémon which seem to appear in real-life locations by use of GPS and the phone's camera.
The craze has seen people Pokémon hunting all over the world, in sometimes controversial circumstances.
In Austria users caused outrage by hunting Pokémon at a memorial to victims of the Nazis in Graz.
And in Spain two Japanese tourists had to be rescued by police after walking into a busy motorway tunnel hunting Pokémon.
On Thursday motoring organization the Swiss Touring Club issued warnings to players in Switzerland who may be taking unnecessary risks.
“Some young and not-so young players are ready to take risks on public roads to capture virtual monsters in a reality that can turn out to be dangerous,” it said in a statement.
It warned of the danger of being distracted by the game when driving and said “inattention and distraction at the wheel form one of the most frequent causes of accidents (nearly a quarter)”.
Drivers should avoid the “big temptation” to play Pokémon in the car, it said, adding that being distracted by a mobile phone increases a person's reaction time by up to 50 percent.
“Pedestrians should also be aware that all sources of distraction place them in danger. It is their responsibility to adopt measured and adequate behaviour when they play.”
For a thorough explanation of how the game works, read this article on Pokémon hunting in Stockholm by our colleagues at The Local Sweden.