After the German occupation of Czechoslovakia in 1939, he was briefly arrested by the Germans but soon released in exchange for a pledge of loyalty. In 1942, after prime minister Eliáš got arrested by Heydrich, Bienert was appointed to minister of interior under the new prime minister Jaroslav Krejčí. In 1945 Bienert replaced Krejčí in this position and at the same time also served as the substitute for seriously ill president Hácha.