Japanese medical academia continues to depend on quantitative indicators, contrary to the general trend in research evaluation. To understand this situation better and facilitate discussion, this study aimed to examine how Japanese medical researchers perceive quantitative indicators and qualitative factors of research evaluation and their differences by the researchers’ characteristics.

We employed a web-based cross-sectional survey and distributed the self-administered questionnaire to academic society members via the Japanese Association of Medical Sciences.

We received 3139 valid responses representing Japanese medical researchers in any medical research field (basic, clinical and social medicine).

The subjective importance of quantitative indicators and qualitative factors in evaluating researchers (eg, the journal impact factor (IF) or the originality of the research topic) was assessed on a four-point scale, with 1 indicating ‘especially important’ and 4 indicating ‘not important’. The attitude towards various opinions in quantitative and qualitative research evaluation (eg, the possibility of research misconduct or susceptibility to unconscious bias) was also evaluated on a four-point scale, ranging from 1, ‘strongly agree’, to 4, ‘completely disagree’.

Notably, 67.4% of the medical researchers, particularly men, younger and basic medicine researchers, responded that the journal IF was important in researcher evaluation. Most researchers (88.8%) agreed that some important studies do not get properly evaluated in research evaluation using quantitative indicators. The respondents perceived quantitative indicators as possibly leading to misconduct, especially in basic medicine (strongly agree—basic, 22.7%; clinical, 11.7%; and social, 16.1%). According to the research fields, researchers consider different qualitative factors, such as the originality of the research topic (especially important—basic, 46.2%; social, 39.1%; and clinical, 32.0%) and the contribution to solving clinical and social problems (especially important—basic, 30.4%; clinical, 41.0%; and social, 52.0%), as important. Older researchers tended to believe that qualitative research evaluation was unaffected by unconscious bias.

Despite recommendations from the Declaration on Research Assessment and the Leiden Manifesto to de-emphasise quantitative indicators, this study found that Japanese medical researchers have actually tended to prioritise the journal IF and other quantitative indicators based on English-language publications in their research evaluation. Therefore, constantly reviewing the research evaluation methods while respecting the viewpoints of researchers from different research fields, generations and genders is crucial.