Nakamura was ordained a priest on 19 March 1988. He was responsible for formation at the minor seminary of the Archdiocese of Nagasaki and parish vicar in Nakamachi. He did additional studies in moral theology in Rome. He returned to his role at the minor seminary, was parish vicar in the cathedral parish of Urakami, and pastor in Togitsu. He was responsible for formation at the major seminary in Fukuoka and then pastor in Uematsu. From 2009 to 2019 he taught moral theology at the major seminaries of Fukuoka and Tokyo. From 2014 to 2019 he was also pastor of Miura-machi.