[Purpose]: To investigate factors contributing to the drastic increase and subsequent decrease in latent tuberculosis infection (LTBI) notifications in 2011 (n = 10,046) and 2012 (n = 8,771), respectively, in Japan. [Methods]: We conducted cross-sectional surveys in all 495 health centers in Japan in 2012 and 2013 using a semistructured questionnaire that contained questions regarding the number of contacts listed for contact investigation, interferon-gamma release assay (IGRA) results, and incident of possible false positive IGRA results. [Results]: Both the numbers and proportion of patients investigated using IGRA tended to increase from 2009 to 2012. However, the numbers and proportion of IGRA-positive patients, as well as that of those with borderline IGRA results, increased in 2011 and have decreased since 2012. In the 2012 survey, only 34 health centers (8%) reported questionable IGRA results. [Discussion]: The removal of the age limit for LTBI treatment in 2010 may have contributed to the increase in the number of LTBI notifications in 2011, as the increase was particularly remarkable in the elderly age group. The increase in the proportion of positive and borderline IGRA results was likely partly due to expanded IGRA coverage that included more medical staff and the older population, which have a relatively high prevalence of tuberculosis infection, as well as a change from second-generation to third-generation QuantiFERON (QFT®) IGRA that offered increased sensitivity. The decrease in the number of outbreak incident cases and infectious patients may have contributed to the decrease in the number of LTBI notifications in 2012. [Conclusion]: Factors such as the increase in the number of patients undergoing IGRA, increase in the number of positive or borderline results due to QFT changes, and decrease in the number of tuberculosis outbreak incidents and infectious patients likely contributed to the increase and decrease in the number of LTBI notifications in 2011 and 2012, respectively.