Swiss International Airlines, a subsidiary of German carrier Lufthansa, confirmed the cancellations of its Geneva-Munich and Zurich-Munich flights on its website.
Flights heading to Frankfurt, Hanover and Dusseldorf will still run but will be subject to delays and cancellations.
The industrial action in Germany is set to hit Frankfurt, Munich, Dusseldorf, Cologne-Bonn, Dortmund and Hanover airports as service workers' union Verdi enters a battle with the government over pay rises for the public sector.
Verdi says that workers deserve a pay raise of six percent, and many German states have seen walkouts at kindergartens, hospitals, town halls and local transport as well.
Workers including mechanics, air traffic controllers, ground crew and administrators are all expected to walk off the job in this latest strike.
But it's the airport firefighters whose walk-out will force the flights to be cancelled at Frankfurt, Munich and Cologne-Bonn.
Without firefighters on duty, no service is possible at an airport.
Wednesday is set to be a day of chaos as no long-haul flights will arrive or depart at Munich airport, with many internal and European services also cancelled.
The strike is set to last until 3pm on Wednesday.
Customers who have booked through Swiss can rebook another flight for no charge or receive a refund.