The Philippines has made huge progress in its goal to eliminate malaria by 2030. Currently, the biggest challenge is bringing down incidence in the province of Palawan, which contributes over 90% of the reported malaria cases in the country. This requires robust and improved surveillance strategies and better diagnostic tools. The aim of this work is to measure malaria infection prevalence using microscopy, rapid diagnostic test (RDTs) and PCR to in order to determine how much malaria is missed by the current passive surveillance. From June 2016 to January 2017, monthly week-long rolling cross sectional surveys were carried out in health facilities providing microscopy and RDT services in Rizal, Palawan. Consenting patients, and their companions, regardless of symptoms, donated finger-pricked blood samples. 3,029 individuals participated in the survey, with their blood samples tested for malaria using the 3 diagnostic tests. Infection prevalence by microscopy, RDT and PCR were 5.05%, 5.81%, and 12.21%, respectively. Almost 12% asymptomatic and 7% sub-patent infections were apparently missed by the routine surveillance, which can potentially serve as infectious reservoir and sustain malaria transmission in the area. Distinct spatial patterns between individuals identified as malaria positive by different diagnostic methods were observed, suggesting some areas of transmission may be missed by reliance on reporting of symptomatic cases alone. Passive incidence of cases reported in health facilities is still the main metric of malaria burden in a particular area in the Philippines, and considering the likely imperfect health-care seeking behavior of the population, screening of asymptomatic family members or household companions during health facility or community surveys, might augment passive clinical surveillance. Acknowledging further the diagnostic limits of microscopy and RDTs, more sensitive, practical and high throughput molecular tools to detect all infections may be considered to supplement and accelerate malaria elimination activities.