The organisational structure of an EMB comprises two key tiers: the policy-making level and the implementation level.

The secretariat often refers to the structure below the policy-making EMB member level, and encompasses the officials in the EMB who are responsible for policy implementation. The secretariat staff may work either part time or full time. These officials are responsible for executing EMB policies and activities, including planning and organising elections. In Governmental Model EMBs, the secretariat almost always is the EMB, and may also assist in making policy under executive branch of government direction. In Independent Model EMBs, the EMB secretariat is the structure below the policy-making EMB member level. In Mixed Model EMBs, a secretariat may service the administrative needs of the policy-making and oversight functions undertaken by the independent component of the EMB, while the governmental component of the EMB is the secretariat for electoral implementation.

Secretariats in Governmental and Mixed Model EMBs may be temporary, or part-time, assuming other duties in periods without electoral activity. In Independent Model EMBs, the secretariat is generally headed by a full-time administrator, with a title such as EMB Chief Executive Officer, Director of Elections, Secretary-General, or Chief Electoral Officer, or the EMB Secretary. In Australia, the person holding this position is called the Electoral Commissioner, and is also a member of the three-person EMB. In some smaller Independent EMBs, there may however not be a full-time secretariat except during election periods, and its secretariat head may have other duties than duties related to elections.

The two tiers are independent in the Independent Model EMB and part of the executive for the Governmental Model EMB. For the Mixed Model EMB, the top tier (policy making level) is Independent from the executive, while the lower implementation level is part of the executive, and usually lies under the Ministry of Interior or the Ministry of Justice.