BACKGROUND: Achieving vector control targets is a key step towards malaria elimination. Because of variations in reporting of progress towards vector control targets in 2013, the coverage of these vector control interventions in Namibia was assessed. METHODS: Data on 9846 households, representing 41,314 people, collected in the 2013 nationally-representative Namibia Demographic and Health Survey were used to explore the coverage of two vector control methods: indoor residual spraying (IRS) and insecticide-treated nets (ITNs). Regional data on Plasmodium falciparum parasite rate in those aged 2-10 years (PfPR2-10), obtained from the Malaria Atlas Project, were used to provide information on malaria transmission intensity. Poisson regression analyses were carried out exploring the relationship between household interventions and PfPR2-10, with fully adjusted models adjusting for wealth and residence type and accounting for regional and enumeration area clustering. Additionally, the coverage as a function of government intervention zones was explored and models were compared using log-likelihood ratio tests. RESULTS: Intervention coverage was greatest in the highest transmission areas (PfPR2-10 ≥ 5%), but was still below target levels of 95% coverage in these regions, with 27.6% of households covered by IRS, 32.3% with an ITN and 49.0% with at least one intervention (ITN and/or IRS). In fully adjusted models, PfPR2-10 ≥ 5% was strongly associated with IRS (RR 14.54; 95% CI 5.56-38.02; p < 0.001), ITN ownership (RR 5.70; 95% CI 2.84-11.45; p < 0.001) and ITN and/or IRS coverage (RR 5.32; 95% CI 3.09-9.16; p < 0.001). CONCLUSIONS: The prevalence of IRS and ITN interventions in 2013 did not reflect the Namibian government intervention targets. As such, there is a need to include quantitative monitoring of such interventions to reliably inform intervention strategies for malaria elimination in Namibia.