The Winterthur prosecutor called for jail terms of six to 15 months, alleging "homicide by negligence".
The collision killed 71 people, most of them Russian schoolchildren. It involved a jet of Russia's Bashkirian Airlines and a DHL cargo plane.
Swiss firm Skyguide controlled flights over southern Germany at the time.
The accused, who were not named by Swiss media, denied responsibility for the collision.
An air accident inquiry last year concluded that a catastrophic chain of human error was to blame. It accused Skyguide of organisational failures contributing to the crash.
The collision happened over a German village near Lake Constance.
The investigators found that a single Skyguide air traffic controller on duty had given the pilots just 43 seconds to act.
The controller was fatally stabbed by a Russian man in 2004, in a suspected revenge attack.
The controller had told the Russian pilots to descend, while their onboard collision avoidance system had told them to climb to avoid the DHL cargo plane.Güncelleme Tarihi: 20 Eylül 2018, 18:16