The Motor Vehicles Department is regulated by the Government of Kerala in terms of policy formulation and its implementation.  The Department is administered by the Transport Commissioner who is the Head of Department. 

The Department has four functional levels

• (i) Head Office under the Transport Commissioner
• (ii) Four Zonal Offices under Deputy Transport Commissioners 
• (iii) Eighteen Regional Transport Offices 
• (iv) Forty two Sub Regional Transport Offices under Joint Regional Transport Officers. 

 In addition, there are 12 Motor Vehicles Border Check Posts headed by Motor Vehicle Inspectors. At the Head Office, one Additional Transport Commissioner, two Senior Deputy Transport Commissioners, one Assistant Transport Commissioner, one Administrative Officer, one Finance Officer, one Law Officer, one Assistant Secretary, one Statistical Officer and one Accounts Officer are there to assist the Transport Commissioner.  In addition, a Technical Advisor also assists him exclusively on matters connected with the control of Automobile Pollution, Computerisation and Modernisation of the Department.