The survey also found that more than 40 percent of married people said they have not had sex in the past month, said Kunio Kitamura, head of the clinic of the Japan Family Planning Association, who took part in the survey.
"This is directly linked with falling birth rate. Policy actions are necessary," Kitamura told AFP.
The data confirmed a wider social belief that younger men are becoming "herbivorous", a label attached to passive men who do not actively seek women and sex.
The latest biennial survey found that 36.1 percent of Japanese males between the ages of 16-19 said they had no interest or even despised sex, a jump from 17.5 percent in the 2008 study.
Compounding the issue was data that showed 59 percent of girls in the same age group felt the same way, up 12 percentage points from 2008.
The data is a worry for a government aiming to encourage couples to have children to reverse a falling birth rate and avert a potential economic calamity.
Japan's total fertility rate in 2009 was estimated by the government at 1.37 births per woman, one of the world's lowest, compared with 2.06 in the United States and 1.97 in France.
The trend has been largely blamed on a widespread belief, especially in rural Japan, that women who give birth should quit their jobs, amid shortages of childcare centres and other systemic factors.
Japan's population has already started to decline as younger people delay starting a family due to the perceived burden on their finances, lifestyles and careers.
A growing population of elderly, known for their longevity, is meanwhile overwhelming a welfare system that is decreasingly supported by a shrinking workforce, meaning that tax revenue is declining.
Collectively, the survey found all age categories showed a general lack of interest toward sex, except for men in their 30-34 years of age with just 5.8 percent of these respondents not interested, as opposed to 8.3 percent in 2008.
The survey also found that 40.8 percent of married people said they had not had sex in the past month, up from 36.5 percent in the 2008 survey and 31.9 percent in the 2004 survey.
Nearly 50 percent of married people older than 40 years old said they have not had sex in the past month, the study said.
Among reasons for not having sex, survey participants cited vague reluctance after childbirth, that they could not be bothered, or that they were too tired after work, it said.
The survey, conducted by a team of experts commissioned by the health ministry, received valid answers from 671 men and 869 women in interviews.
It was originally designed to gauge the success of Japan's birth control education with an aim to reduce unwanted pregnancies, Kitamura said.
But the falling abortion rate may be a result of a general indifference toward sex and not attributable to the success of sex education, he said.