The national carrier Swiss has temporarily suspended 52 pilots on the grounds that their anxiety about their future with the company could affect cockpit safety.
The company, which is in the process of being taken over by Germany's Lufthansa, has started disciplinary proceedings against the pilots, who had complained in an open letter to management.
Swiss spokesman Jean-Claude Donzel told swissinfo that the pilots – who fly Saab 2000 aircraft and are based at Basel airport - had complained that stress caused by the uncertain climate could affect their flying ability.
"The pilots said in the letter that this was a stressful situation for them, which could lead to a lack of safety in the cockpit," Donzel said.
He said the individuals concerned would undergo an assessment of their flying abilities as soon as possible. If they pass, the pilots will be allowed to resume their duties.
He added that the uncertainty stemmed from a Swiss announcement in January that the Saab 2000 machines would no longer fly from Basel from October 30, as part of cost-cutting measures.
Donzel said that Swiss "had to react to keep our customers safe and it was better to suspend these pilots".
As a result of the suspension, six flights were cancelled on Monday – including one to Brussels and two to Munich – affecting 60–90 passengers. The spokesman added that this had not disrupted business to any great extent.
"We could afford [to cancel the flights] because the load is very low in business class during July and August," Donzel said.
The Swiss Pilots' Association said it was shocked that the pilots had been suspended.
Spokesman Martin Gutknecht said that the open letter was a "cry for help" and it was regrettable that Swiss had reacted by instigating disciplinary proceedings.
A total of 72 pilots fly the Saab 2000 aircraft. Twenty did not sign the open letter.
"The other pilots who did not sign the letter have already told their colleagues that they feel fine and can fly," Donzel said.
The pilots affected and Swiss management are set to meet on Monday to discuss the situation.
The Saab 2000s fly from Basel to Brussels, Munich, London, Düsseldorf and Madrid and cover a small number of holiday destinations in southern Europe.
swissinfo, Faryal Mirza
Swiss owns seven Saab 2000s, which operate out of Basel and are flown by 72 pilots.
Swiss announced in January that it would reduce its fleet by 13 planes to 62 and 800-1,000 jobs would be lost by 2006.
The Saabs will be taken out of service from October 30.
Full-time pilot posts for the European region will fall from 440 to 207.