Prior to the creation of PPA, port administration in the Philippines was merged with the traditional function of revenue collection of the Bureau of Customs (BOC).

Around this time, the Bureau of Customs had proposed to the Reorganization Committee and to Congress the creation of a separate government agency to integrate the functions of port operations, cargo handling, and port development and maintenance to enable the Bureau to concentrate on tax and customs duties collection.

513, the salient features of which were the granting of police authority to the PPA, the creation of a National Ports Advisory Council (NPAC) to strengthen cooperation between the government and the private sector, and the empowering of the Authority to exact reasonable administrative fines for specific violations of its rules and regulations.

By virtue of its charter, the PPA was attached to what was then the Department of Public Works and Highways' responsibility.

On August 24, 2007, the Philippine Supreme Court (per 24-page decision by Angelina Sandoval-Gutierrez), ordered the PPA to pay 231 residents of Batangas City the just compensation sum of P6 billion as payment of 185 lots it bought in 2001 for the construction of Phase 2 of the Batangas Port Zone.