In July 1939, he participated in the opening of the Central Agency for Jewish Emigration in Prague, where his immediate superior was SS-Sturmbannführer Hans Günther.

At the beginning of 1940, Eichmann brought Novak with him to the RSHA in Berlin and put him in his new office, the Eichmannreferat, on "Jewish matters and evacuations".

Novak handled the technical problems of organizing deportation trains "resettling" Poles and Jews from the incorporated territories to the General Government in 1940–41; he requisitioned railcars from Deutsche Reichsbahn for deportation and coordinated with it the hours of passages of these trains in coordination with the SS, police and concentration camp officials.

[2] Novak also worked closely with other leaders of the "Jewish question" in other countries, such as Theodor Dannecker, Alois Brunner and Dieter Wisliceny.

By the end of the war, Novak had organized at least 260 trains from Germany, Austria and the Protectorate, at least 147 from Hungary, 87 from the Netherlands, 76 from France, 63 from Slovakia, 27 from Belgium, 23 from Greece, 11 from Italy, 7 from Bulgaria and 6 from Croatia — more than 707 from western and southern Europe.

On 17 December 1964, the jury did not convict for aiding and abetting murder, but sentenced him to eight years in prison only because of Article 87 of the Austrian penal code known as the "Railroad Acts", committing the criminal offense of intentionally compromising the integrity of the passengers during transport by not providing adequate water, food and toilet facilities.

Simon Wiesenthal later calculated that Novak spent three minutes and twenty seconds in custody for each victim whom he sent to his or her death at Auschwitz.