In spite of its shortcomings, the Ki-21 remained in service until the end of the war, being utilized as transport (along with the civil transport version MC-21), bomber crew and paratrooper trainer, for liaison and communications, special commando and secret missions, and kamikaze operations.
Meskipun dengan kelemahan-kelemahan itu, Ki-21 tetap bertugas hingga akhir perang, difungsikan sebagai transport (bersama dengan versi transport sipil MC-21), pelatihan awak pengebom dan pasukan para, misi-misi komando khusus dan rahasia, dan operasi-operasi kamikaze.