Local Government Act Article 77

If there are disputes over authority between the central government, special municipalities, and counties/cities, such disputes shall be resolved by the Legislative Yuan. If there are disputes over self-government matters between counties and townships/cities, such disputes shall be resolved by the Ministry of the Interior in consultation with the relevant central competent authorities.If there are disputes over authority between special municipalities or between special municipalities and counties/cities, such disputes shall be resolved by the Executive Yuan. If there are disputes over authority between counties/cities, such disputes shall be resolved by relevant central competent authorities. If there are disputes over authority between townships/cities, such disputes shall be resolved by the county government.
中文原文 地方制度法第77條
中央與直轄市、縣(市)間,權限遇有爭議時,由立法院院會議決之;縣與鄉(鎮、市)間,自治事項遇有爭議時,由內政部會同中央各該主管機關解決之。
直轄市間、直轄市與縣(市)間,事權發生爭議時,由行政院解決之;縣(市)間,事權發生爭議時,由中央各該主管機關解決之;鄉(鎮、市)間,事權發生爭議時,由縣政府解決之。

English translation for reference only; the Chinese text prevails. Not legal advice.