In its initial establishment, the ASEANSAI Secretariat shall be headed by The Head of Secretariat, which shall be appointed by the Chairman of ASEANSAI, due to the secretariat follows where the Chairman’s resides.

In 2013, the Assembly’s decided to restructure the Secretariat for the sustainability of ASEANSAI in the future. It was agreed that there would be a transitional arrangement before the establishment of permanent secretariat and administration office could take place which would be marked by the signing of the Amendment of the ASEANSAI Agreement

The arrangement was that The Audit Board of The Republic of Indonesia would continue its secretariat duties in managing finance and bank account, keeping records, and communicating with donors, while the administration support duties to the ASEANSAI Executive Committee would be provided by the SAI who served as the Chairman of ASEANSAI.

In 2016, through the signing of the protocol on amending the ASEANSAI Agreement, restructuring of the Secretariat become the longer-term Secretariat with six years tenure was approved. During transitional period, the Assembly agreed to retain the existing Secretariat to continue its work until the appointment of the new Secretariat.

At the 4th ASEANSAI Summit 2017, the Audit Board of the Republic of Indonesia was elected as the Secretariat for the period of 2018 – 2023. In 2023, the Audit Board of the Republic of Indonesia was re-elected as the Secretariat of ASEANSAI for the period of 2024 – 2029 at the 7th ASEANSAI Summit.