Musa is administrated by a civil, lay, nonprofit association, and is under the coordination of an Administrative Council composed of permanent members and members elected by the associates. The Administrative Council is responsible for indicating the museum directory.

Administrative Council – 2018-2022 four-year term

Alfredo Wagner B. de Almeida – Soc. Brasileira para o Progresso da Ciência (SBPC)
Bernardo M. de Paula – ManausCult
Celdo Braga – Conselho Municipal de Cultura
Dyson Teles – Universidade Federal do Amazonas (UFAM)
Efrem Jorge Gondim Ferreira – Instituto Nacional de Pesquisas da Amazônia (INPA)
Ingo Wahnfried – Universidade Federal do Amazonas (UFAM)
Jair Maia – Presidente
João Valsecchi do Amaral – Instituto Mamirauá
Lúcia H van Velthem – Museu Paraense Emilio Goeldi (MPEG)
Marcio Silva de Lira – Secretário
Maria Paula Mourão – Universidade do Estado do Amazonas (UEA)
Orsine Oliveira Junior – AmazonasTur
Urias Sergio de Freitas – Associação Comercial do Amazonas (ACA)
Wilson Luiz B. Périco – Centro da Indústria do Estado do Amazonas (CIEAM)