Bustamante's first term as unofficial leader of the government was dogged by controversy. While taking on the role of head of the BITU, he was also leader of government business. In 1947 and 1948, he was elected as mayor of Kingston. In 1947 he was arrested with Frank Pixley and put on trial for manslaughter at the courthouse in Port Maria. He was acquitted. In 1952 he was arrested by the American authorities while he was on official business in Puerto Rico.