Indonesia has a long history as Maritime Country. In the past, Maritime Kingdoms of the archipelago such as Sriwijaya, Majapahit, the kingdom in Maluku held the key to world trade routes through spices. Traders from Gujarat and China took spices from the Maluku Islands and then sent them via merchant ships to China, the Arabian Peninsula, Europe, to Madagascar.

Small ports in Indonesia became transit points and trading centers that brought together the traders from various nationalities, thus becoming big trading ports. This is the background of the birth of the Indonesian Port in the era of independence.

Previously, to manage ports in Indonesia, 4 Pelindos were formed and divided into different regions. Pelindo I, for example, managed ports in the Provinces of Nanggroe Aceh Darussalam, North Sumatra, Riau and the Riau Islands. Pelindo I was formed based on PP No. 56 of 1991, while the name Pelindo I was determined based on Notarial Deed No. 1 dated December 1, 1992.

Pelindo II managed ports in 10 provinces, namely West Sumatra, Jambi, South Sumatra, Bengkulu, Lampung, Bangka Belitung, Banten, DKI Jakarta, West Java and West Kalimantan. Pelindo II was established based on PP No. 57 of 1991, Pelindo II (Persero) was established based on the Notary Deed of Imas Fatimah SH, No. 3, dated December 1, 1992.

Pelindo III managed ports in 7 provinces, namely East Java, Central Java, South Kalimantan, Central Kalimantan, Bali, NTB and NTT. The establishment of Pelindo III is stated in the Deed of Notary Imas Fatimah, SH No. 5 dated December 1, 1992, based on PP No. 58 of 1991.

Meanwhile, Pelindo IV managed ports in 11 provinces, namely East Kalimantan, North Kalimantan, South Sulawesi, Central Sulawesi, Southeast Sulawesi, Gorontalo, North Sulawesi, Maluku, North Maluku, Papua and West Papua. Pelindo IV was formed based on PP No. 59 dated October 19, 1991. While the deed of formation was Deed of Notary Imas Fatimah, SH no. 7 dated December 1, 1992.

Each Pelindo has branches and subsidiaries to manage its business. Pelindo I, II, III, IV are non-listed state-owned enterprises (BUMN) whose shares are 100% owned by the Ministry of SOEs as the State Shareholders of the Republic of Indonesia. Therefore, there is no information on the Major Shareholders or Individual Controlling Shares in Pelindo. The Republic of Indonesia, represented by the Ministry of State-Owned Enterprises of the Republic of Indonesia, is the sole owner and sole shareholder.

The merger or integration of the four Pelindos into one Pelindo, which was later named PT Pelabuhan Indonesia, was based on Peraturan Pemerintah Nomor 101 Tahun 2021 About Integration of PT Pelindo I, III, dan IV (Persero) to PT Pelabuhan Indonesia II (Persero);. 

Pelindo II act as a holding parent (the parent company) and all three Pelindo (I, III, IV) acts as sub-holding. The establishment of sub-holdings that manage business clusters is aimed at increasing Pelindo's service capacity and business efficiency.