On 27 September 1939, the SD and SiPo (made up of the Gestapo and the Kripo) were folded into the new Reich Main Security Office or Reichssicherheitshauptamt (RSHA), which was placed under Heydrich's control. The title of Chef der Sicherheitspolizei und des SD (Chief of Security Police and SD) or CSSD was conferred on Heydrich on 1 October. Heydrich became the president of the International Criminal Police Commission (later known as Interpol) on 24 August 1940, and its headquarters were transferred to Berlin. He was promoted to SS-Obergruppenführer und General der Polizei on 24 September 1941.
Heydrich created the "Zentralstelle IIP Polen" unit of the Gestapo in order to coordinate the ethnic cleansing of Poles in "Operation Tannenberg" and the Intelligenzaktion, two codenames for extermination actions directed at the Polish people during the German occupation of Poland. Among the 100,000 people murdered in the Intelligenzaktion operations in 1939–1940, approximately 61,000 were members of the Polish intelligentsia: scholars, clergy, former officers, and others, whom the Germans identified as political targets in the Special Prosecution Book-Poland, compiled before the war began in September 1939.
When Hitler asked for a pretext for the invasion of Poland in 1939, Himmler, Heydrich, and Heinrich Müller masterminded a false flag plan code-named Operation Himmler. It involved a fake attack on the German radio station at Gleiwitz on 31 August 1939. Heydrich masterminded the plan and toured the site, which was about four miles from the Polish border. Wearing Polish uniforms, 150 German troops carried out several attacks along the border. Hitler used the ruse as an excuse to launch his invasion.
On Himmler's instructions, Heydrich formed the Einsatzgruppen (task forces) to travel in the wake of the German armies at the start of World War II. On 21 September 1939, Heydrich sent out a teleprinter message on the "Jewish question in the occupied territory" to the chiefs of all Einsatzgruppen with instructions to round up Jewish people for placement into ghettos, called for the formation of Judenräte (Jewish councils), ordered a census, and promoted Aryanization plans for Jewish-owned businesses and farms, among other measures. The Einsatzgruppen units followed the army into Poland to implement the plans. Later, in the Soviet Union, they were charged with rounding up and killing Jews via firing squad and gas vans. Historian Raul Hilberg estimates that between 1941 and 1945 the Einsatzgruppen and related auxiliary troops killed more than two million people, including 1.3 million Jews. Heydrich ensured the safety of certain athletes, such as Paul Sommer, a Jewish German champion fencer he knew from his pre-SS days, and the Polish Olympic fencing team that competed at the 1936 Summer Olympics.
On 29 November 1939, Heydrich issued a cable about the "Evacuation of New Eastern Provinces", detailing the deportation of people by railway to concentration camps, and giving guidance surrounding the December 1939 census, which would be the basis on which those deportations were performed. In May 1941 Heydrich drew up regulations with Quartermaster general Eduard Wagner for the upcoming invasion of the Soviet Union, which ensured that the Einsatzgruppen and army would co-operate in murdering Soviet Jews.