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Abstract Background Since the scale-up of routine viral load (VL) testing started in 2016, there is limited evidence on VL suppression rates under programmatic settings and groups at risk of non-suppression. We conducted a study to estimate VL non-suppression (> 1000 copies/ml) and its risk factors using "routine" and "repeat after enhanced adherence counselling (EAC)" VL results. Methods We conducted an analytic cross-sectional study using secondary VL testing data collected between 2014 and 2018 from a centrally located laboratory. We analysed data from routine tests and repeat tests after an individual received EAC. Our outcome was viral load non-suppression. Bivariable and multivariable logistic regression was performed to identify factors associated with having VL non-suppression for routine and repeat VL. Results We analysed 103,609 VL test results (101,725 routine and 1884 repeat test results) collected from the country’s ten provinces. Of the 101,725 routine and 1884 repeat VL tests, 13.8% and 52.9% were non-suppressed, respectively. Only one in seven (1:7) of the non-suppressed routine VL tests had a repeat test after EAC. For routine VL tests; males (vs females, adjusted odds ratio (aOR) = 1.19, [95% CI 1.14–1.24]) and adolescents (10–19 years) (vs adults (25–49 years), aOR = 3.11, [95% CI 2.9–3.31]) were more at risk of VL non-suppression. The patients who received care at the secondary level (vs primary, aOR = 1.21, [95% CI 1.17–1.26]) and tertiary level (vs primary, aOR = 1.63, [95% CI 1.44–1.85]) had a higher risk of VL non-suppression compared to the primary level. Those that started ART in 2014–2015 (vs