As an apostle, Cowley visited various church missions throughout the world, spoke in many conferences, and helped direct other church affairs. A few months later, in March 1946, he suffered a heart attack. Although he recovered enough to resume his church assignments, he was never as "robust in health" as before. In December 1946, Cowley was assigned as president of the church's Pacific Missions, a newly created position in which he oversaw several missions, including the Hawaiian, Central Pacific, Samoan, Tongan, Tahitian, Australian and New Zealand missions.