The helicopter, a leased aircraft operated by Helicopter Wing 64, went down during a routine flight exercise, the ministry said, adding that search and rescue teams continued searching for the remains of the third crew member.
"The deaths of the crew members hit me and the entire Bundeswehr hard," Defence Minister Boris Pistorius said.
Bundeswehr's General for Aviation Safety will lead the investigation in close cooperation with civilian authorities, the ministry added.
(Reporting by Riham Alkousaa; Editing by Chizu Nomiyama )

LEIPZIG, GERMANY - MAY 18: Soldiers of the Bundeswehr, Germany's armed forces, unload an NH90 transport helicopter from a plane Antonov AN-124 for military transport arriving from Afghanistan at Leizpig Airport on May 18, 2021 in Leipzig, Germany. Germany has begun pulling out its approximately 1,100 remaining troops from Afghanistan in accordance with the general withdrawal of NATO forces. A total of 53 Bundeswehr soldiers have been killed in Afghanistan since 2002. (Photo by Jens Schlueter/Getty Images)