In Japan, attention has increasingly focused on ensuring the quality of care, particularly in the area of cancer care. The 2006 Basic Cancer Control Act reinforced efforts to ensure the quality of cancer care in a number of sectors, including the role of government in ensuring quality. We initiated a government-funded research project to develop quality indicators to measure the quality of care for five major cancers (breast, lung, stomach, colorectal, and liver cancer) in Japan, and palliative care for cancers in general. While we successfully developed a total of 206 quality indicators, a number of issues have been raised regarding the concepts and methodologies used to measure quality. Examples include the choice between measuring the process of care versus the outcome of care; the degree to which the process-outcome link should be confirmed in real-world measurement; handling of exceptional cases; interpretation of measurement results between quality of care versus quality of documentation; creation of summary scores; and the optimal number of quality indicators for measurement considering the trade-off between the measurement validity versus resource limitations. These and other issues must be carefully considered when attempting to measure quality of care, and although many appear to have no correct answer, continuation of the project requires that a decision nevertheless be made. Future activities in this project, which is still ongoing, should focus on the further exploration of these problems.