When in April 1941 Soviet NKVD arrested the commander of the ZWP in the Vilnius region, general Nikodem Sulik, it was Krzyżanowski who de facto replaced him, and his position was officially confirmed by general Stefan Rowecki in August.
Transferred to Regional Office of Military Preparation in Toruń, he finally ended up in the Border Protection Corps (KOP) units located along eastern border of the Second Polish Republic.