As a consequence of various changes made between the prototypes and the pre-production aircraft, the "M.S.406" designation was adopted for the type. On 3 February 1938, the first pre-production aircraft made its first flight; during December 1938, the final pre-production M.S.406 was delivered. The pre-production aircraft served to build up experience of both manufacturing and testing of the type in advance of production M.S.406s. These 15 aircraft were used for various purposes, such as the third and tenth which served as examples for subcontractors Société nationale des constructions aéronautiques de l'ouest (SNCAO) and Société nationale des constructions aéronautiques du Midi (SNCAM), and the twelfth and thirteenth functioned as prototypes for the Swiss D-3801 and D-3800 export models. Multiple variants of the aircraft, including some which later entered mass production, were first represented amongst the pre-production aircraft.