Microsoft sold 53,547 units of the Xbox 360 in the four weeks to September 28, compared with 33,071 units of the PS3, data from Enterbrain showed on Friday.
Nintendo maintained its leading position in the Japanese console market, having sold 109,548 units of the Wii during the month.
Although popular in the United States, the Xbox 360 has been struggling to compete with the PS3 and the Wii in Japan, home to both Sony and Nintendo.
In a bid to lift sales, Microsoft on September 11 cut the price of the Xbox 360 Arcade, which comes without a hard disk drive, by 8,000 yen ($76) to 19,800 yen. It also lowered the price of the high-end Elite model by 8,000 yen to 39,800 yen.
Sony sells the PS3 with a 40-gigabyte hard disk drive for 39,980 yen, while Nintendo offers the Wii for 25,000 yen.
In the handheld video game market, Nintendo sold 234,477 units of its DS, compared with 109,274 units of Sony's PlayStation Portable.
Sales of the PSP seem to have slowed ahead of the planned launch on October 16 in Japan of a new model of the portable machine, Enterbrain said.
The new PSP-3000 will come with a built-in microphone and advanced LCD panel that is better suited for use outdoors and offers a shorter response time than the existing machine.
Nintendo will launch a new DS on November 1 that can take pictures and play music.