Background In many countries, epidemiological surveillance of chronic diseases is monitored by local registries (LR) which do not necessarily cover the whole national territory. This gap has fostered interest in using non-registry databases (e.g., health care or mortality databases) available for the whole territory as proxies for incidence at the local level. However, direct counts from these databases do not provide reliable incidence measures. Accordingly, specific methods are needed to correct proxies and assess their epidemiological usefulness. Methods This study’s objective was to implement a three-stage turnkey methodology using national non-registry data to predict incidence in geographical areas without an LR as follows: constructing a calibration model to make predictions including accurate prediction intervals; accuracy assessment of predictions and rationale for the criteria to assess which predictions were epidemiologically useful; mapping after spatial smoothing of the latter predictions. The methodology was applied to a real-world setting, whereby we aimed to predict cancer incidence, by gender, at the district level in France over the 2007–15 period for 24 different cancer sites, using several health care indicators and mortality. In the present paper, the spatial smoothing performed on predicted incidence of epidemiological interest is illustrated for two examples. Results Predicted incidence of epidemiological interest was possible for 27/34 solid site-gender combinations and for only 2/8 haematological malignancies-gender combinations. Mapping of smoothed predicted incidence provided a clear picture of the main contrasts in incidence between districts. Conclusions The methodology implemented provides a comprehensive framework to produce valuable predictions of incidence at a district level, using proxy measures and existing LR.