A panel including architects and an official from the Japan Toilet Association sifted through nearly 400 applications before settling on two dozen municipalities and companies with the loveliest latrines.
The criteria for the inaugural award were cleanliness, safety, comfortableness, novelty/creativity, and sustainability.
The range of winners included firms that created makeshift toilets after Japan's 2011 quake-tsunami disaster, Haneda airport for its spotless restrooms, and the organisers of a toilet-themed art festival.
Others got the nod for making female restrooms more attractive, including supplying space for breast-feeding and shortening waiting lines.
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But the government insists the award was more than just a beauty contest -- it was about empowering women.
"Pleasant restrooms will improve the quality of daily life and encourage women's empowerment," Haruko Arimura, minister in charge of women's empowerment, told an awards ceremony on Friday.
"Having public toilets where women feel safe is a sign of the maturity and richness of a society."
That idea was panned on social media.
"I cannot believe the government has created the toilet award. Are restrooms the reason why Japanese women cannot shine?" said one Twitter user.