1. Operation and Regulatory Division

The are two units under the Operation and regulatory Division. This is the main division in the Johor Port Authority. The reason is that the tasks and functions of JPA as a regulatory body to the ports under its supervision need units in the operation division to exercise control so as to ensure that the port operators carry out their work in accordance with the relevant acts and based on the terms of the agreements made:-

Safety and Security Unit 

There are three sub units in this Unit i.e the fire and Rescue unit, Dangerous Cargo Unit and Security Unit. The responsibilities are more to regulating and monitoring the safety and security of the port operation.

Fire and Rescue Unit

The main focus in this unit is to ensure the compliance of port users to the guidelines on all aspects of fire safety as stipulated in the term and conditions of the Permit To Work (PTW) issued by licensed operators. In addition, this unit also ensure the fire Safety Installations (FSI) are in good working order, that the FSI undergo  regular inspection and regular training is conducted on its usage to ensure that the Fire and Rescue Unit is able to respond to an emergency and the fire-fighters of the licensed operators are able to operate the FSI.

Dangerous Cargo Unit

The role of this unit is to carry out regulating and enforcement pertaining to the handling of dangerous cargo efficiently and effectively. It establishes facilities for a simple and practical system of declaring dangerous cargo by setting up groups for handling such cargo.

Security Unit

This unit is responsible for enforcing rules and laws on the premises of the Johor Port Authority from time to time, maintaining port security conditions that are conductive and safeguarded from criminal thereat, ensuring that the security services of port operators  .

Marine Unit

The main functions of this unit are to ensure a high level of efficiency in the pilots at the ports under its supervision and to issue licenses to support services and private jetties. Moreover, this units is responsible for ensuring that all marine activities in the Johor Port area always adhere  to the requirements of the laws and regulations laid down for operations, though patrolling and enforcement.

2. CORPORATE SERVICE AND DEVELOPMENT DIVISION

Corporate Services and Marketing Unit

The Corporate Services Unit is JPA's communication body in charge of corporate matters, marketing, promotion and facilitation of commerce in port under its supervision. It is also the source of comprehensive information fro JPA, enabling the organization to carry out its functions and play its role effectively.

Development Unit

The development unit is responsible for supervising the maintenance of all JPA's immovable assets and monitoring physical development in the ports by implementing and maintaining development projects under the Federal and Johor Port Authority.

Information Resource Development Unit

This unit applies information technology usage in JPA's daily business, enhancing work efficiency and effectiveness through the potential provided by advancement in information and communication technology. it controls, administrates, monitors and keeps abreast of current advancement in information and communication technology so as to be more organized, systematic and competitive, it follows by closely the use of ICT (Information Communication Technology).

3. MANAGEMENT SERVICE AND FINANCE DIVISION

Management Service Unit

The Administration Unit manages office administration matters to ensure smooth running of the system of delivery  and support towards realizing the functions of the organization. It also manages and developed human resources so as to fulfill the needs of the organization in carrying out its functions and responsibilities.

Finance Unit

Efficiently and transparent management of financial resources in accordance with the rules that have been laid down is the main function of this unit.

Property Unit

The Property Unit has the role of supervising and developing port land. It surveys the property of the ports (around) and adds to JPA's assets through outright purchase, application for government land and land reclamation.

4. INTERNAL AUDIT UNIT

This unit helps the management to carry out good administrative management based on directives and rules in line with objective and practice of sound management.

5. LEGAL UNIT

The Legal unit has the role of helping the management to fulfill their responsibilities in accordance with the implementation of laws pertaining to the Johor Port Authority and the Johor Port Authority (Tanjung Pelepas) and to carry out tasks related to the work of the JPA and JPA(TP) Boards of Director.