The education ministry has asked all 81 private and public medical schools to check their admission procedures for possible discrimination against female applicants.
Authorities said they would also check the gender ratio of successful applicants for the past six months, confirming it was the first ever such nationwide investigation.
"If their answers are judged as not reasonable, we will ask additional questions or visit them directly," a ministry official said, adding that the results of the probe would be published as early as next month.
The probe came after a Tokyo medical school admitted it routinely altered entrance test scores for female applicants to keep women out, in a scandal that has sparked outrage in Japan.
The alterations reportedly stretched back as far as 2006 and apparently aimed to keep the ratio of women in the school at 30 percent or lower.
Newspaper headline: Probe after Tokyo med school excludes women