Vajra is a family-owned company managed by an Advisory Board that consists of a team of professionals. The Board normally meets every three months, and more frequently when situations demand. For instance, the Board currently meets every week on Tuesdays. This is in consideration of the sudden change in management and administration systems due to the rapid expansion of the company in the recent past. It helps the company in making fast decision without having to wait for the quarterly meetings. 

The whole administration is divided into three Departments headed by Directors: Department of Engineering & Construction (DEC); Department of Corporate Services (DCS); and Vajra Construction & Service Center (VCSC). DEC is further divided into four Divisions looked by General Managers: Infrastructure Division (ID); Mechanical, Electrical, and Plumbing Division (MEPD); Hydropower Division (HPD); and Mechanical Division (MD).  DCS has three Divisions managed by a General Manager each: Finance Division (FD); Procurement Division (PD); and Human Resources & Administration Division (HRAD). VCSC consists of eight Sections: Fabrication & Production Section (FPS); Store & Procurement Section (SPS); Tools & Equipment Section (TES); Mechanical Service Section (MSS); Training & Apprenticeship Section (TAS); Facility Management Section (FMS); Research & Development Section (RDS); and Quality, Health, Safety, and Environmental Section (QHSES).