Who administers direct democracy mechanisms at the national level?

Chief Electoral Officer is in charge of administering referendums

The Constitutional Polls Act 1977 section says that any constitutional ?poll shall be taken in the same manner as if it were a general election of members of the Niue Assembly and the Assembly Act 1966 and any other law relating to such elections, as far as they are applicable, shall apply accordingly?.  The Assembly Act 1966 show that the Chief Electoral Officer (a government official but appointed by the independent Public Service Commission) runs elections.

ConstitutionalPolls Act 1977 

http://www.paclii.org/nu/legis/consol_act/cpa1977268/

Article3. Subject to this Act and any regulations made under it, and subject to allnecessary modifications, the poll shall be taken in the same manner as if itwere a general election of members of the Niue Assembly and the Assembly Act1966 and any other law relating to such elections, as far as they areapplicable, shall apply accordingly.