Who administers direct democracy mechanisms at the national level?

Referendum Act (amended date: 2018/01/03)

Article 3. The competent authority for national referendums is the Central Election Commission, which is responsible for directing and supervising municipal or county (city) election commissions.

The competent authority for local referendums is the corresponding municipal government or county (city) government.

During the referendum period, the election commissions of specific levels may call on the staff of the governments of specific levels and the faculty of public schools to handle related affairs. The said governments, public schools, and their assigned staff and faculty shall not refuse without due reason.

Civil Servants Election And Recall Act (amended date: 2018/05/09)

Article 7. The Central Election Commission shall be in charge of the election of members of the Legislative Yuan, municipal councilors, the governors of municipalities (municipal mayors), county (city) councilors and governors of counties (cities) and direct and supervise each of each municipal or county (city) election commission. […]

Article 9. The recall of civil servants shall be implemented by the election commissions of specific levels, and the provisions of Article 7 shall apply mutatis mutandis.