Issues of sub-national referendums regulated at the national level

Japan
Constitution of Japan
(Cameinto effect May 3, 1947; not amended since)
http://www.kantei.go.jp/foreign/constitution_and_government_of_japan/constitution_e.html
Article 95. A special law,applicable only to one local public entity, cannot be enacted by the Dietwithout the consent of the majority of the voters of the local public entityconcerned, obtained in accordance with law.