It knocked last week's number one, Dreamgirls, out of pole position, while newcomer Ghost Rider rode into the number four slot. The latest installment in Toei's One Piece animated franchise opened in second place.
Shochiku launched Genghis Khan on 440 screens, the widest ever release for a local title, topping the studio's previous record of 354 screens with hit Love And Honour.
While a sampling of 25 of the country's major theatres showed an 18% increase over producer Haruki Kadokawa's previous comeback success Yamato on opening day, the final weekend tally fell well short of the WWII drama.
Considering Genghis Khan is a historical epic about another culture and without a huge name cast attached, the studio is positive about the film's prospects, pegging final earnings above $20m.
Shochiku acquired domestic and worldwide rights to the film in January, with the film's co-producer Avex Entertainment handling Asian sales. Shochiku brought the film to Berlin 's European Film Market and secured deals with over 50 countries.
Kadokawa had been developing Genghis Khan for some 27 years. Shot over four months on location, the filme cost over $25m and features thousands of Mongolian extras. It has been timed to celebrate the 800th anniversary of Mongolia 's foundation.
The film is directed by Shinichiro Sawai and stars Takashi Sorimachi (Yamato) and Rei Kikukawa (Godzilla: Final Wars).