Background: This study aimed to examine possible effects of implementing a national query program on site-specific cancer mortality rates. Materials and Methods: A total of 2,874 query letters were sent out by the Department of Statistics, Ministry of Health and Welfare of Taiwan between January 2009 and December 2011 to medical certifiers who reported "neoplasm with uncertain nature" on the death certificate asking for more detailed information for coding. Results: Of the 2,571 responses, in 1,398 cases (54%) medical certifiers were still unable to determine the nature of the neoplasm. There were four neoplasm sites for which more than 50% of the responses changed the category to malignant, the gastrointestinal system (73%), urinary system (60%), stomach (55%) and rectum (53%). The liver was the cancer site that showed the largest absolute increase in the number of deaths after the query; however, the brain showed the largest relative increase, at 12%. Conclusions: Different neoplasm sites showed different magnitudes of change in nature after the query. Brain cancer mortality rates exhibited the largest increase.