1. Human Resources Division - J1. Role in joint operations to manage manpower, distribution and administration of personnel in terms of individual aspects such as discipline, courses, morale, welfare, religious and legal aspects in peacetime and war of assigned forces under the auspices of the Joint Forces Headquarters.
2. Intelligence Division - J2. Role is to plan, collate, process and disseminate intelligence at operational level to the needs and uses of the joint operation. It is also responsible for advising the Joint Force Commander in all aspects of intelligence co-operation.
3. Operations Division - J3. Role is to plan, coordinate and control all operations and joint, integrated and combined exercises. It also serves to align the needs of MAF involvement in UN missions.
4. Logistics Operations Division - J4. Responsible for preparing and coordinating all aspects of logistical assistance to support operations and joint exercises, integrated and implemented in a combination of MAF with other government, law enforcement agencies and the armed forces of friendly countries. This section works closely with MAF Logistics Services Headquarters to coordinate and provide logistical requirements to assigned forces involved in operations and in joint and combined exercises.
5. Financial Management. Responsible for managing the financial expenses in JFHQ in compliance with existing financial procedures of and enhance the use of online financial system that has been in force.
6. Contingency Planning Division - J5. Responsible to the Joint Force Commander in formulating contingency defense plans for future military operations within and outside of the country and assessing the real capabilities of current MAF operations. This division is responsible for proposing an increase in the ability of MAF and JFHQ based on contingency plans and the actual operation of the MAF HQ - Defense Planning Division. At the same time, the Division will also formulate policies and strategies of national defense planning and to develop a balanced, integrated and credible Joint Force to defend the country. It is also responsible for evaluating and implementing the MAF Contingency Plans.
7. Civil Military Cooperation Cell. Responsible as liaison between the military and the public, to assist the military coordinate assistance needed from the public and help the public to coordinate the necessary aid to the military, or more simply as the focal point in JFHQ on matters relating to the public by the military.
8. Information Systems and Communications Division - J6. Serves to provide all the necessary electronic communications and facilities needed for Joint Force operations and administration. This includes planning, coordinating and preparing all government communications needs of JFHQ up to the formation of assigned forces. It must be able to fulfill the execution of all joint and multinational operations. The division is also responsible for building the capacity of government communications required by MAF in the future including the ability of Electronic Warfare. The assignment includes the responsibility to design, build, manage and maintain all computing needs and information management at JFHQ.
9. Exercise Division - J7. Role is to plan and control all aspects of Joint and Combined exercises involving MAF in order to enhance the level of preparedness and ability of forces to the highest level to support the National Defense Policy.
10. Military Health Division - J9. Role in providing medical matters in terms of safety and health of personnel, deployment management, operations, training plans, communications, interoperability, joint training, modernization of forces, structure and distribution of resources. The division is also responsible for issuing directives and guidelines in all medical matters related to operations and to focus on the consolidation of daily operational tasks for staff operations, doctrine, training, development of combat, base operations support and resources.
11. JFHQ Camp. Responsible for assisting the management of administrative and logistical aspects of JFHQ as well as to accommodate and support the Operational Level Command conducted by all Divisions, Branches and Cells in JFHQ organization.
12. Secretariat. Serves as a coordinating centre for all aspects of the administration between MINDEF, MAF HQ, Service HQs and other outside agencies that deal with JFHQ as well as coordinating the needs of intermediaries between JFHQ.
13. Public Affairs Division. Responsible for determining the security and regularity of information distributed to the media, to advise, assist and coordinate the needs of the media, especially in the publication of matters relating to exercises and operations that should be known by the public.
14. Strategic Management Cell. Responsible for aspects which include strategic management, innovation and quality, Key Performance Index, performance evaluation through the management audit JFHQ SRS and preparation for MAF Committee Meetings for Excellence and Innovation and the Working Committee for Excellence and Innovation.
15. Markas Angkatan Tugas Bersama 2. Role specialized in command and control of all the assets of Operation PASIR Area of Responsibility, which also involves deployment of assets from all three branches of the Malaysian Army, Royal Malaysian Navy and Royal Malaysian Air Force placed under Operational Control. MK ATB 2 also represents a garrison integrating all members and assets from all the three branches of service in joint efforts to combat and prevent all forms of threat either internally or externally that can affect the safety and sovereignty at Eastern Sabah coastline.