and 9.5% of men between 35 and 39 reported having no sexual experience.
Researchers at the University of Tokyo say the findings are partly linked to social and economic status - poorer men were more likely to be virgins than those on high salaries.
Men with lower incomes were up to 20 times more likely to be virgins than their wealthier counterparts.
Cyrus Ghaznavi, the study's lead author, said: "Although the discussion around cause and effect becomes very complex when considering who becomes sexually experienced and who remains a virgin, we show that heterosexual inexperience is at least partly a socioeconomic issue for men.
"Simply put, money talks."
The virginity rate among both men and women in Japan has almost doubled since 1992, with adults in their 30s up to 10 times more likely to be virgins compared to British, Australian and Americans where the rate of virginity is between one and 5%.
The research involved between 11,000 and 18,000 adults and was carried out by the Japanese National Institute of Population and Social Security Research between 1992 to 2015.
By 2015, 8.9% of heterosexual women and 9.5% of men between the ages of 35 and 39 reported having no sexual experience.
The new analysis is Japan's first national estimate of virginity and its most detailed analysis of data from the National Fertility Survey of Japan.
The survey goes further than previous studies as it takes into account the age and socioeconomic status of people who have never had straight sex.
Mr Ghaznavi said: "The most informative aspect of sexual inactivity involves those who have opted out of or are, for some reason they cannot control, excluded from the mating market, regardless of their previous sexual experience."
Men were more likely to have had sex if they had permanent, full-time jobs and lived in cities with more than a million people, Mr Ghaznavi said.
But women on lower incomes were more likely to have had sex than their male counterparts who earned the same amount of money.
The study's authors believe this may be because married women in Japan are more likely to have had sex and be full-time housewives without a salary.