Machimura was elected to his first term in the House of Representatives in the December 1983 election, and he was re-elected in each election since. He became Minister of Education, Science, Sports and Culture on 11 September 1997, as part of Prime Minister Ryutaro Hashimoto's second cabinet, and became State Secretary for Foreign Affairs on 31 July 1998, in Keizō Obuchi's first cabinet. In March 2000, he became Special Advisor to the Prime Minister, serving under Obuchi and his successor, Yoshirō Mori. On 5 December 2000, he became Minister of Education, Science, Sports and Culture and Director-General of the Science and Technology Agency, before becoming Minister of Education, Culture, Sports, Science and Technology on 6 January 2001.