The International Dzogchen Community of Namgyalgar is managed by a local governance structure called a Gakyil ("mandala of joy"),  a collective body divided into three sections: economic and administrative activities, work activities, and cultural and educational activities. These sections correspond to the body, energy, and mind, respectively.  The Gakyil operates without hierarchy. Members, ranging from three to nine, are elected annually in accordance with the constitution.

In addition to local Gakyils, there is an International Gakyil responsible for overall  management and coordination of activities globally.

The Gakyil’s structure reflects three types of activities: economic and administrative tasks (body), work activities and cooperatives (energy), and cultural and educational teachings (mind). The Gakyil operates with the flow of energy, symbolizing the influx of combined efforts and the spread of benefits to all beings.

The International Dzogchen Community of Namgyalgar is registered with the Australian Charities and Not-for-profit Commission (ACNC) and has Tax deductible status for donations made toward the building and maintenance of Namgyalgar, as an education centre for Buddhist studies and Tibetan culture. 

The Ati Yoga Foundation  and the Shang Shung Institute of Australia  are affiliated organisations.  The Ati Yoga Foundation unites all the organizations of the Dzogchen Community internationally.  The Shang Shung Institute preserves and promotes Tibetan culture.