The Empresa Nacional de Puertos S.A. – ENAPU, S.A. is the port authority for the Port of Iquitos. Before it was created, Peruvian ports were under different authorities from the Ministry of Property and Commerce to individual organizations that administered separate ports. In 1968, the Harbor National Corporation was created, but it never began operations.

Under the name ENAPU PERU, La Compania Nacional de Puertos S.A., began operations in 1970 as a public entity under the Transport and Communications Sector. The Port of Iquitos is one of the eastern ports under the jurisdiction of ENAPU. ENAPU administers, operates, and maintains the relevant harbor terminals and supports the development of foreign trade and territorial integration.

The Port of Iquitos contains two wharves. Wharf No. 1 is 114 meters long and 15.4 meters wide, and Wharf No. 2 is 72 meters long and 15.36 meters wide. The wharves contain 11 berths for shallow-draft vessels and four anchorage points in the river.

In 2008, the Port of Iquitos welcomed 5532 vessels carrying a total of 244.8 thousand tons of cargo, including 55 thousand tons of exports, 71.3 thousand tons of imports, and 118.5 thousand tons of cabotage. The Port of Iquitos handled 122 containers, including 22 containers of exports, 23 containers of imports, and 77 containers of cabotage.

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