The administration of Chagpori is done by the Governing Board. The day-to-day work is carried out by the director and the office. The Institute is registered as a non-profit charitable organization under the West Bengal government.

In Tibet, Chagpori came under the direct guidance of the Private Office of HH the Dalai Lama, so it was important for Dr Trogawa Rinpoche to offer Chagpori to the present Dalai Lama. After accepting, the Private Office decided that Chagpori should come under the control of the Health Department of the Central Tibetan Administration of the Tibetan Government in exile.