Background: The scale-up of effective malaria control in the last decade has resulted in a substantial decline in the incidence of clinical malaria in many countries. The effects on the proportions of asymptomatic and submicroscopic infections, and on transmission potential are yet poorly understood. Methods: In Papua New Guinea, vector control has been intensified since 2008, and improved diagnosis and treatment introduced in 2012. Cross-sectional surveys were conducted in Madang Province in 2006 (n=1280), 2010 (n=2117) and 2014 (n=2516). Infections were quantified by highly sensitive qPCR and gametocytes by RT-qPCR. Results: P. falciparum prevalence by qPCR decreased from 42% in 2006 to 9% in 2014. P. vivax prevalence decreased from 42% in 2006 to 13% in 2010, but then increased to 20% in 2014. Parasite densities decreased 5-fold from 2006 to 2010; 72% of P. falciparum and 87% of P. vivax infections were submicroscopic in 2014. Gametocyte density and positivity correlated closely with parasitemia, and population gametocyte prevalence decreased 3-fold for P. falciparum and 29% for P. vivax from 2010 to 2014. Conclusions: Sustained control has resulted in reduced transmission potential but an increasing proportion of gametocyte carriers are asymptomatic and submicroscopic and represent a challenge to malaria control.