Introduction Influenza morbidity and mortality are significant in the countries of South America, yet influenza vaccination is as low as 56.7% among pregnant women, reaching 76.7% of adults with chronic diseases. This article measures the relative values for the vaccination hesitancy indicators of confidence, complacency and convenience by risk-groups in urban areas of five countries of South America with contrasting vaccination rates, analyzing their association with sociodemographic variables and self-reported immunization status. Methods An exit survey was applied to 640 individuals per country in Brazil, Chile, Paraguay, Peru and Uruguay, distributed equally across risk groups of older adults, adults with risk factors, children ≤6 and pregnant women. Indicators were constructed for vaccine confidence, complacency and convenience. Analysis of variance and multiple logistic analysis was undertaken. Results Adults with risk factors are somewhat more confident of the influenza vaccine yet also more complacent. Convenience is higher for mothers of minors. Children and older adults report higher levels of vaccination. The 3Cs are more different across countries than across risk groups, with values for Chile higher for confidence and those for Uruguay the lowest. Complacency is lower in Brazil and higher in Uruguay. Results suggest that confidence and complacency affect vaccination rates across risk groups and countries. Conclusions Influenza vaccine confidence, complacency and convenience have to be bolstered to improve effective coverage across all risk groups in the urban areas of the countries studied. The role played by country contextual and national vaccination programs has to be further researched in relation to effective coverage of influenza vaccine.