Reported incidence of the zoonotic malariaPlasmodium knowlesihas markedly increased across Southeast Asia and threatens malaria elimination. Nonzoonotic transmission ofP. knowlesihas been experimentally demonstrated, but it remains unknown whether nonzoonotic transmission is contributing to increases inP. knowlesicases. Here, we adapt model-based inference methods to estimateRC, individual case reproductive numbers, forP. knowlesi,P. falciparumandP. vivaxhuman cases in Malaysia from 2012–2020 (n = 32,635). Best fitting models forP. knowlesishowed subcritical transmission (RC< 1) consistent with a large reservoir of unobserved infection sources, indicatingP. knowlesiremains a primarily zoonotic infection. In contrast, sustained transmission (RC> 1) was estimated historically forP. falciparumandP. vivax, with declines inRCestimates observed over time consistent with local elimination. Together, this suggests sustained nonzoonoticP. knowlesitransmission is highly unlikely and that new approaches are urgently needed to control spillover risks.