These attacks continued even after the March 1939 German occupation, because Vlajka was disappointed with their lack of prominence in the Protectorate of Bohemia and Moravia and felt that anti-Jewish policies were not severe enough.

The Vlajka became politically unacceptable after another traitor, Emanuel Moravec, was appointed the Minister of Education in the government of Protectorate in January 1942.

He was often and openly criticized and fiercely denounced by Vlajka members for being a former legionary, an officer of the Czechoslovak Army and an alleged Freemason.

At the end of 1942, Vlajka was disbanded and some of its leaders, including Jan Rys-Rozsévač, were held in the Dachau concentration camp as privileged prisoners.

Towards the end of the war they even formed the so called Voluntary Company of St. Wenceslaus, the only Waffen-SS unit composed of volunteers of Czech ethnicity (which nevertheless was never involved in any fight).