The COVID-19 pandemic highlighted critical gaps in the Philippine health laboratory system, including limited testing capacities, insufficient trained personnel, and inadequate resource distribution. To address these issues, the Philippine government established the Office for Health Laboratories (OHL) and sought technical assistance from the Japan International Cooperation Agency (JICA) through the Project for Strengthening the Philippine National Health Laboratory Network for Infectious Diseases (PHeLNIDs). This project aims to enhance the National Health Laboratory Network's (NHLN) capacity for infectious disease surveillance and response. Phase 1 of the PHeLNIDs project included focus group discussions (FGDs) conducted across 17 regions to assess challenges and develop recommendations for a tier-based laboratory network. Key findings revealed logistical, workforce, transportation, and data management challenges that hinder the effectiveness of specimen referral workflows. Recommendations emphasized decentralizing diagnostic capabilities through subnational reference laboratories, strengthening logistics, and implementing an Integrated Laboratory Information Management System (ILIMS). This article underscores the importance of laboratory decentralization, capacity building, and improved resource management to enhance laboratory-based surveillance and response to emerging infectious diseases. The proposed interventions aim to bolster the Philippine laboratory network, reduce turnaround times, and improve public health outcomes.