Background We assessed the impact of two major modifications of the Dutch National Influenza Prevention Programme – the introduction in 1997 of free‐of‐charge vaccination to persons aged ≥65 years and to high‐risk groups (previously only advised, and not free of charge), and the lowering of the eligible age to 60 years in 2008 – on the estimated incidence of influenza infection leading to influenza‐like illness ( ILI ). Methods Additive negative‐binomial segmented regression models were fitted to ILI data from GP sentinel surveillance in two‐eight‐season intervals (1993/4 to 2000/1, 2004/5 to 2011/12, comparing pre‐ and post‐policy‐change periods within each interval), with laboratory virological reporting of samples positive for influenza or other ILI ‐causing pathogens as covariates. Results For the 2008 policy change, there was a significant step decrease in influenza contribution considering all ages (=−111 per 100 positives; 95% CI : −162, −65·0), <60 years and 60–64 years age groups ( B = −92·1 per 100; 95% CI : −134, −55·5; B = −5·2; 95% CI : −10·3, −1·2, respectively). There was no evidence for a decrease associated with the 1997 policy change targeting the ≥65 years age group. Conclusions In the Netherlands, a 56% reduction in influenza contribution was associated with the 2008 policy targeting 60–64 year‐olds, but there was no effect of the earlier policy targeting ≥65‐year‐olds, for whom vaccination coverage was already rising before the policy change.