PEZA’s PTOPS: A New Era of Digital Governance for Ecozone Enterprises

Transacting with the Philippine Economic Zone Authority (PEZA) for over two years, I have found its processes consistently convenient and efficient. One thing I particularly appreciate is PEZA’s use of online processes and systems, such as email submissions for applications and online payment portals. Even with the effectiveness of its previous systems, PEZA continues to push forward to further simplify and enhance the ease of doing business in the Philippines.

This is especially timely with the implementation of the Corporate Recovery and Tax Incentives for Enterprises to Maximize Opportunities for Reinvigorating the Economy (CREATE MORE) Act which broadens and enhances the tax incentives available to registered business entities (RBEs) while clearly specifying the requirements for availment.

This year, PEZA introduced PEZA – The One Portal System (PTOPS), a centralised database platform designed to automate and streamline core PEZA processes. To note, PTOPS has 3 modules to be rolled out in phases: (1) Business Enterprise Registration Management System (BERMS); (2) Permits Management System (PMS); and (3) Logistics Management System (LMS).

Phase 1: BERMS

On 08 April 2025, through Memorandum Circular No. 2025-021, PEZA officially launched BERMS, the Phase 1 Module of PTOPS. This web-based platform improves the registration and certification processes and record-keeping for ecozone enterprises, ecozone developers and service enterprises. It facilitates the issuance of electronic certificates, such as Certificate of Registration, VAT Zero-Rating Certificate, and Certificate of Entitlement to Tax Incentive (CETI), among others, and supports online payments, application reviews and real-time monitoring.

To support the rollout of BERMS, PEZA issued Memorandum Order Nos. 2025-006 and 2025-013 detailing the implementation guidelines, including user manuals and operational procedures. These issuances provide clear instructions for both existing and prospective ecozone enterprises on how to navigate the platform.

The mandatory use of BERMS for the issuance of VAT Zero-Rating Certificates and CETIs took effect on 01 May 2025, while its use for enterprise registration became mandatory on 16 August 2025.

Below is an overview of the registration and certification process under the BERMS module in PTOPS.

1. Account activation/enrollment - To access the applications under BERMS, existing RBEs must activate their account in PTOPS, while proponent enterprises must complete the enrolment process.
2. Submission of application with supporting documents - Depending on the type of application, the enterprise-applicant needs to fill out the online application forms and upload the necessary supporting documents as provided under the PEZA Citizen’s Charter. Once submitted, a QR code and reference number are generated, which can be used to check the status of the application. 
3. Pre-screening - The application will be subject to pre-screening to ensure completeness of documents and correctness of information prior to official acceptance by PEZA. 
4. Payment of fees - If the application is compliant, it will be tagged for payment of the applicable fees. On the other hand, if the application is incomplete or non-compliant, it will be tagged as deemed not filed and the enterprise-applicant will have to comply with the necessary documents and re-submit the application. 
5. Further review and evaluation - After payment, the application will be subject to further review by the concerned division of PEZA depending on the type of application (ex. Enterprise Registration Division for registration applications). 
6. Generation of certificates - If the application is approved, the enterprise-applicant will be able to generate the electronic copy of the certificates in PTOPS. Otherwise, PEZA will encode in PTOPS the corresponding remarks/comments explaining the disapproval. 

Note that certain applications will be endorsed for PEZA Board approval (with investment capital of less than ₱15,000,000,000.00) or to the Fiscal Incentives Review Board (with investment capital of more than  ₱15,000,000,000.00).

Phase 2: PMS

Following BERMS, PEZA recently launched and provided guidelines for the implementation of Phase 2 or the PMS, under Memorandum Order No. 2025-014. The PMS integrates the three systems of PEZA, i.e., the Electronic Import Permit System (ePIS), the enhanced Automated Export Documentation System (eAEDS) and the electronic Zone Transfer System (eZTS), currently managed by three Value Added Service Providers involving the required permits for the movement of goods. The mandatory use of PMS for the approval of import permits began on 01 September 2025.

Conclusion 

With the anticipated release of the final module, i.e., LMS, PEZA’s PTOPS is nearing full implementation. The centralisation and automation of key processes, such as securing the VAT zero-rating certificate, which confirms the registered business enterprise’s compliance with the conditions of VAT zero-rating on local purchases and must be applied every year, will significantly ease the compliance burden for RBEs.   

PTOPS marks a transformative shift in PEZA’s commitment to enhance transparency, reduce administrative burden, and improve turnaround times for ecozone stakeholders.

As published in BusinessWorld, dated 21 October 2025