Who administers direct democracy mechanisms at the national level?

Citizens Initiated Referenda Act 1993

( Enacted on 28 September 1993)

http://www.legislation.govt.nz/act/public/1993/0101/latest/DLM317193.html?search=ts_act%40bill%40regulation%40deemedreg_citizens_resel_25_h&p=1

Article 26A(2).

TheGovernor-General must issue a writ in form 2A of the Scheduleto the Electoral Commission requiring the Electoral Commission to conduct theindicative referendum.

Article 26(2).

TheGovernor-General must issue a writ in form 2 of the Scheduleto the Electoral Commission requiring the Electoral Commission to make allnecessary arrangements for the conduct of the indicative referendum.

Electoral Act 1993

(Enacted in 17August 1993, last amended in 1 July 2012)

http://www.legislation.govt.nz/act/public/1993/0087/latest/DLM307519.html

Article4C.

Theobjective of the Electoral Commission is to administer the electoral systemimpartially, efficiently, effectively, and in a way that—

(a) facilitatesparticipation in parliamentary democracy; and

(b) promotesunderstanding of the electoral system and associated matters; and

(c) maintainsconfidence in the administration of the electoral system.

Article7.

TheElectoral Commission must act independently in performing its statutoryfunctions and duties, and exercising its statutory powers […]

Section 26A(2) of the CitizensInitiated Referenda Act 1993 requires the Governor General to issue a writrequiring the Electoral Commission to make all necessary arrangements forindicative referenda conducted by postal voting.  Section 26(2) applies to indicative referendaconducted other than by postal voting.