OBJECTIVES: In Japan, introduction of economic evaluation of health policy issues such as pricing and reimbursement of drugs and medical devices is gaining attention; several research guidelines have been proposed for the same. We compared the key features of these guidelines and obtained suggestions for future research. METHODS: We reviewed literature using the Ichushi database (Japanese medical literature database) and the database on government-funded research reports, and also contacted investigators and experts for related information. RESULTS: Four guidelines were identified: Shiragami (2004) and Kamae (2007) groups, funded by the Ministry of Health and Welfare, Japan, proposed two guidelines on pharmaceutical pricing. The task force of the Ministry of Economy, Trade and Industry, Japan (2007) proposed one guideline on medical device policy. The Hirota group (2011), funded by the Ministry of Health and Welfare, Japan, proposed one guideline on vaccination strategy. Although the headings and structures of all guidelines were almost similar, significant differences were identified among them. For example, two guidelines recommended societal perspective, while the other two recommended consumer’s perspective. In terms of outcome measures, QALYs were preferred in three guidelines, whereas one recommended “the proportions of patients who achieved target clinical results within 2 years.” Trial use was not conducted to verify the feasibility of guidelines, except for the Hirota guideline for vaccination policy. In addition, some recommendations had a serious problem in terms of scientific rationality. CONCLUSIONS: There are significant variations in the key features among all four abovementioned guidelines, and even between the two sets of guidelines for pharmaceutical pricing decisions. To use an economic evaluation to aid rational resource allocation, official guidelines should be established with scientific rigor and integrity, and future discussions about feasibility are needed among various representatives from government, academia and industry.