The Moto-Ki Association certifies qualifying academies after they have completed extensive training in not only the application of Moto-Ki but also in its training methods. These academies are then licensed to train practitioners and submit requests for their certification through the Moto-Ki association.

Valid certificates are signed, stamped, contain a registration number, and have an expiration date (typically 5 years after issuance).

Training is structured into a multi-tier system, starting with three separate majors. The first is designed for individuals who wish to integrate the techniques in with other modalities and provide a service as an intuitive guide, life coach, or energy-counselor. The second major is for the professional energy-healer. Level III of this section is for extending the healing methods to a force capable of clearing a structure or property. The third major is for martial arts instructors.

Instructor level training is available at the higher levels. It is possible to be certified as an instructor within a specific major, or a Master instructor covering all majors. The latter covers mastery of all energy work taught within the Moto-Ki system.

Basic instructor level within a particular major entitles that individual the right to train and offer certification in all levels below Instructor. Master Instructor requires completing all levels of all majors followed by an internship and additional training. Master level instructors are provided the additional wisdom needed to teach and certify instructors.