Since 2014, imported cases of malaria have been notified by SINAVE, the Portuguese nationwide electronic surveillance system that replaced paper-based notification. Nevertheless, the disease is still believed to be under-reported. Completeness of notification of malaria cases in 2016 was estimated using a two-source capture-recapture method, with SINAVE and the Diagnostic-Related Group cases. Completeness of SINAVE and the diagnosis-related group sources was computed in 32.9% and 72.3%, respectively. The results confirm that malaria is under-reported and highlight the need for more effective notification strategies, especially given the risk of resurgence of locally acquired cases.