Who administers direct democracy mechanisms at the national level?

Political Constitution of 1982 (Constitución Política de 1982)with amendments in 2012

https://www.constituteproject.org/constitution/Honduras_2012.pdf

Article 51

There will be a SupremeElectoral Tribunal, autonomous and independent, with juridical personality, with jurisdiction andcompetence in all the Republic, whose organization and functioning will be established by this Constitutionand the Law, which will equally establish that relative to the other electoral organisms, foreverything relative to the electoral acts and procedures.

The law that regulateselectoral matters, may only be reformed or abrogated by the qualified majority of two-thirds of [the] votesof the totality of the members of the National Congress, which must

solicit the prior resolutionof the Supreme Electoral Tribunal, when the initiative does not derive from it.

Special Law on Regulations for Referendums, issued on July 2009(Ley especial que regula el plebiscito y el referendo).

http://aceproject.org/ero-en/regions/americas/HN/honduras-ley-plebicito-y-referendo-2009/view

Article 9.1

Competen al Tribunal Supremo Electoral, de manera exclusiva, lasatribuciones siguientes:

1)      Convocar, organizer y dirigir lasconsultas a los ciudadanos y ciudadanes de caracter nacional. Para elloaplicara en lo pertinente las disposiciones de la Ley Electoral y de lasOrganizaciones Politicas. Con relacion a las consultas de caracter municipal seaplicara lo dispuesto en la Ley de Municipalidades y su respectivo Reglamento;

2)     El Tribunal Supremo Electoral ordenara la publicacionen el Diario Oficial “La Graceta” de los resultados del Plebiscito y delReferendo, indipendientemente de comunicarlo por escrito al Congreso Nacional;y,