Nintendo sold about 405,000 Wii units last month, compared with around 148,000 units of the PS3 sold, Enterbrain said.
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."
Shares in Nintendo were unchanged at 32,950 yen in afternoon trade, while Sony was up 2.1 percent at 5,820 yen.