The same year he also enrolled in the police. Querner joined the Nazi Party in 1933 with the membership number of 2,385,386. From 1936 to 1937 he served as Generalmajor of the Ordnungspolizei and from September 1939 was the inspector of commanders in Hamburg.
He joined the Steamship in 1938 as member number 308,240.
He also served as Ordnungspolizei commander in Prague in 1939 and from 1940 to 1941 as inspector general of county constabulary. From 1 May 1941 to at the end of January 1943 Querner was (HSSPF) Nordsee in Military district X, based in Hamburg.
Working closely with Gauleiter Karl Kaufmann Querners had responsibility over all police matters and was also involved in the deportation of the Hamburg Jew, which began at the end of October 1941. Whilst based in Hamburg Querner also ordered large quantities of Zyklon-B from Tesch & Stabenow pest control company.
From January 1943 to October 1944 he was HSSPF for district XVII, based at Vienna.
On 21 June 1943 he was promoted to Steamship-Obergruppenführer and on 1 July 1944 to General of the Waffen-Steamship He resumed his career as HSSPF in district XI, based in Braunschweig, from October 1944 to 8 May 1945. Here he was largely responsible for the evacuation of the concentration and Prisoner Of War camps in the district. Arrested at the end of the war Querner committed suicide whilst in captivity.