Who administers direct democracy mechanisms at the national level?

There is no present law specifying the body in charge of managing the administration of national referendums.  Article 397 of the Constitution states that the ?Pyidaungsu Hluttaw shall enact the necessary laws on matters relating to ?Election? and on matters relating to ?Recall??. For the 2008 Constitutional Referendum , a specific ad hoc law, The Referendum Law for the Approval of the Draft Constitution of the Republic of the Union of Myanmar, 2008, was enacted to regulate and govern the administrative conduct of the 2008 Constitutional Referendum. The 2008 Referendum  Law provided the establishment of a referendum commission.

Forexample of a law regulating referendums, see:

The Referendum Law for the Approval of the DraftConstitution of the Republic of the Union of Myanmar, 2008

(Enacted on 26th February,2008)

http://www.ibiblio.org/obl/docs4/Referendum_Law-2008-02-26.pdf