After the invasion and breakup of Yugoslavia, on 10 April 1941 authorities of Independent State of Croatia gave him the rank of a rear admiral and appointed him commander of naval forces. He remained in that capacity until 17 September 1943. However, during that time he mainly served as military attaché in Berlin because the Rome Treaty of 1941 forbade the Independent State of Croatia to form a navy. As attaché he served until November 1942 when he became a liaison officer with 7th SS Volunteer Mountain Division Prinz Eugen. Jakčin had that duty until September 1943. In September 1943 he was appointed Croatian Ambassador to Bulgaria in Sofia, where he suddenly died in March 1944 of natural causes.