Lembaga Pelabuhan Johor or the Johor Port Authority (JPA) was established on the 1st of January 1975 under the Port Authorities Act 1963. JPA commenced operations in 1977 and is the first port in Malaysia that features a free trade zone. Since its establishment, JPA has experienced a remarkable progress. In 1995, port operations were privatized under the Privatization Act 1990 and JPA began to function as a regulatory body for the operations carried out in the port.

Due to the need of meeting high demand, coupled with the limited coastal area in Pasir Gudang, the Government has taken steps to open up another port in Tanjung Pelepas, on the west region of the state. The government has also given approval to a private company to plan, build, operate and manage the port. The second port project started in 1995. In 1999, phase 1 was completed and began its operation in October 1999.

Johor Port Authority is also responsible for managing the Tanjung Belungkor Ferry Terminal (TFTB) in Kota Tinggi and Changi Ferry Terminal (TFC) in Singapore. Both terminals have been built to promote tourism activities in Desaru and was commissioned on 8th of September 1993. The first RORO ferry service was carried out by Ferrylink until 8th of April 2002. The RORO ferry services has been discontinued and only scheduled passenger ferry operates between the two terminals. Passenger ferry services are currently provided by Limbungan Maju. While Tanjung Belungkor Ferry Terminal is now managed by Marina Island Venture Capital Sdn. Bhd.

Apart from routes to Singapore Changi Ferry Terminal, Tanjung Belungkor Ferry Terminal also provides passenger ferry services to Batam and Tanjung Pinang in Indonesia.