Wii and PS3, made by two of the biggest players in the $30 billion global video game industry, went on sale late last year in a three-way showdown with Microsoft Corp.'s Xbox 360.
A wider range of software titles for the Wii is luring more users, while the PS3's higher price tag is hindering sales growth, Enterbrain said.
The basic model of the PS3 sells for 49,980 yen ($415.9) in Japan, double the price for the Wii.
Nintendo has sold a total 1.4 million units of the Wii in Japan, far outpacing the 614,000 PS3 units sold, Enterbrain said.
"There could be a price cut for the PS3 by the end of the year, and more software titles will hit the market. I expect the PS3 to be doing better after a while," Enterbrain President Hirokazu Hamamura said.
"Of course, the Wii will keep running ahead all the while."