The figure comes amid a high-profile row in Japan that has pitted a young female researcher against the scientific establishment, and after repeated calls for Tokyo to boost female participation in the workforce to help plug a skills gap in the economy.
A nationwide study by the internal affairs ministry found that in March last year there were a record 127,800 female scientists in Japan, accounting for 14.4 per cent of the total and up 0.4 percentage points from a year earlier.
Despite being a personal best for Japan, the percentage is the lowest among countries with comparable data in the Organisation for Economic Co-Operation and Development (OECD), sometimes called the rich nations' club.
In Russia it was 41.2 per cent in 2012, 37.7 per cent in Britain in 2011, 34.9 per cent in Italy in 2011 and 33.6 percent in the United States in 2010.
The Japanese figure, released yesterday, is also lower than Germany's 26.7 per cent, France's 25.6 per cent and South Korea's 17.3 per cent, all in 2011.
Haruko Obokata, whose work was published in the British journal "Nature", outlined a way to change adult cells into the basic material for any body tissue, potentially offering a ready supply of transplant organs.
Obokata's research was hailed as revolutionary, but much of the popular media coverage focused on the fact that she is a young woman in a world dominated by middle-aged men, with newspapers and television offering profiles that concentrated on her supposed feminine charms.
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