At the outbreak of the war with Japan, he was the Commander of an important naval base in Soerabaja. He realised the invasion of Java was just a matter of time, and started to prepare the evacuation of naval personnel to Ceylon or Australia. When the time came, there was more or less a plan ready for execution. Koenraad and his staff embarked on the submarine K-XII, which made it to Australia safely in March 1942, and from there he left for England. Upon returning to Australia Koenraad replaced Rear-Admiral (Acting) F.W. Coster as Flag Officer in charge of all Dutch naval forces in the area. with headquarters in Melbourne, from 1 May 1943 to 1 October 1945; until November 1943 he was also Deputy Commander of Dutch East Indies Armed Forces. After having been temporarily promoted to Rear Admiral, this appointment became effective on 1 November 1943. From 6 October 1945 to 21 January 1946, Koenraad continued his task as the Acting Commander of the Navy in the Dutch East Indies, with its headquarters in Batavia. On 1 May 1946, he retired, being at the same time promoted to the honorary rank of Vice-admiral.