The circumstances of Kaczmarz's death are unclear. In early September 1939, after World War II broke out, he was called up for Polish military service as a reserve lieutenant. He sent a letter to his wife on 4 September and was not heard from afterwards. Theories for his death include the possibility that he died soon after near Nisko (the source of his last letter to his wife) in a German bombing raid on a train he was traveling in, that he died later that month in combat against the Germans near Umiastów, or that he was murdered by the NKVD in April or May 1940 as part of the Katyń massacre.