The findings show that the proportion of virgins in the country, which is also home to the world's oldest population, is growing.
In the latest round of the survey, around 42 percent of the men and 44.2 percent of the women admitted they were virgins, The Japan Times reported on Friday.
The numbers of virgins are higher than in 2010, when the last study was conducted and when only 36.2 percent of men and 38.7 percent of women said they had never had sex,
The study, conducted by the National Institute of Population and Social Security Research, showed that 70 per cent of unmarried men and 60 per cent of unmarried women are not in a relationship.
When the study was first conducted in 1987, the proportion of unmarried men and women who said they had no partner stood at 48.6 per cent and 39.5 per cent, respectively.
The institute has conducted the same survey every five years since then.
The increase in singles was particularly high for people in their late 20s, the age at which fertility in women is thought to be at its peak.
Although 30 per cent of the 2,706 men sampled and 26 per cent of the 2,570 female respondents said they were not currently looking for a relationship, nearly 90 per cent of the respondents said they want to get married but do not really know when.
"They want to tie the knot eventually. But they tend to put it off as they have gaps between their ideals and the reality," Futoshi Ishii from the National Institute of Population and Social Security Research was quoted as saying.
"That's why people marry later or stay single for life, contributing to the nation's low birthrate," Ishii noted.
