The Agency is headed by a Director, who is appointed and discharged by the President of the Republic of Macedonia. The Director is appointed for a four-year term of office.

The Director is held answerable for his/her work and for the work of the Agency to the President of the Republic of Macedonia.

The Government of the Republic of Macedonia may request accountability from the Director about the work of the Agency. The Director of the Agency adopts an act for the organisation and work, and for the systematisation of the jobs in the Agency, upon a prior agreement by the Government of the Republic of Macedonia.