The population estimates at regency level I obtained using the Indonesia 2000 census (10%) (also using the online tabulator) do not match what for example is reported in wikipedia or other websites. It work instead with the 2010 census. Are there some issues with the 2000 census?
The data for the 2000 Indonesian Census geographic identifiers were obtained directly from the Indonesian census office. The period in which these data were collected and tabulated represent a time of significant geographic transition for Indonesia, which may contribute to the differences you are seeing from different sources. Also, since the estimates generated by IPUMS-International are based on sample data, it is not likely that these figures will match exactly, especially for smaller geographic areas.