A well-coordinated and reliable system for the collection and transportation of clinical and environmental specimens are required for effective outbreak control. This manual outlines a structured national framework that connects the Epidemiology and Disease Control Division (EDCD), Provincial Health Directorates, Rapid Response Teams, and laboratories at all levels—public and private—under the technical leadership of the National Public Health Laboratory (NPHL). It provides clear guidance to ensure that specimens are collected, packaged, labeled, stored, and transported in a manner that preserves their integrity, maintains chain of custody, and adheres to established biosafety and biosecurity standards. This document defines referral pathways, coordination mechanisms, and roles within the broader alert, response, and surveillance systems. As a dynamic and complementary resource aligned with existing disease-specific and regulatory guidelines, this manual supports timely diagnosis, strengthens surveillance, and enhances evidence-based public health decision-making. Adherence to these standardized procedures is therefore essential to ensure the accuracy of laboratory results, safeguard health workers and communities, and enable prompt and effective public health actions.