Immigration Commissioner Andrea Domingo identified the wanted man as Yoshinobu Degchi, 34, and his companion Michio Okano, 60, who were nabbed at their apartment in Navotas City.
Domingo said that the duo will be deported for overstaying as they failed to extend their visa after arriving as tourists several months ago.
The immigration chief said the suspects both have missing fingers, the mark of members of the Japan-based criminal syndicate.
Deguchi, Domingo said, has been on the wanted list of Japanese authorities since last year when a warrant for his arrest was issued by the Tokyo police department.
He is wanted for stealing a vehicle and other items worth ¥1.154 million at a parking lot in Mihama-ku Chiba City, Japan on April 29 last year.
The suspect fled to the Philippines a few months later.
Members of the Tokyo police are expected to arrive in Manila within the week to escort the suspects back to Japan. — Rey Arquiza