Who administers direct democracy mechanisms at the national level?

Denmark, The Ministry for Economic Affairs and the Interior, Elections and Referenda in Denmark, accessed 20 July 2019
"The Ministry for Economic Affairs and the Interior is responsible for performing tasks in connection with general elections, referenda, elections to local and regional councils as well as elections of Danish members to the European Parliament. The ministry also manages the political party subsidy scheme of the central government and acts as secretariat to the Election Board and the Eligibility Board."