Yoshitaka Kuroki, 65, a resident of Kawasaki in Kanagawa Prefecture is suspected of having paid 370,000 yen (about $3,600) to the two men on May 10 and 11. One of them was identified as Isao Matsumoto, 64.
The woman escaped from Kuroki's home in Kawasaki's Takatsu ward on May 14 to seek help from the Philippine Embassy in Tokyo.
The two men, who were arrested earlier for selling another Filipina to a different Japanese man, have admitted to selling the woman to Kuroki, who has denied paying for her, police sources said.
The men told investigators that they have arranged 20 to 30 cases of international marriage, the sources said