PEZA is a government corporation attached to the Department of Trade and Industry. It is governed by a 13-man Board, chaired by the Secretary of the Department of Trade and Industry, and composed of 12 other members, 9 of which are Undersecretaries of various Departments whose functions contribute to the successful operation of economic zones. The Board is responsible for the formulation and implementation of policies, plans and programs of the Authority, including the establishment and enforcement of rules and regulations and standards governing the establishment and operation of economic zones.
The Director General is the Vice Chairman of the Board and the Chief Executive Officer of PEZA.
The Director General holds the rank of a Department Undersecretary and is appointed by the President of the Republic of the Philippines.