The Finn finished 0.104secs ahead of Aprilia's Hector Barbera, with Kallio's team-mate and Motegi winner for the past two seasons, Hiroshi Aoyama, third. Alex de Angelis completed a provisional front row covered by 0.276secs.
Andrea Dovizioso carried Japanese honour with fifth for home manufacturer Honda, just ahead of title leader and reigning champion Jorge Lorenzo.
First qualifying – Motegi:1. Kallio (KTM)
2. Barbera (Aprilia) +0.104secs
3. H. Aoyama (KTM) +0.189secs
4. de Angelis (Aprilia) +0.276secs
5. Dovizioso (Honda) +0.364secs
6. Lorenzo (Aprilia) +0.374secs
7. Simon (Honda) +0.496secs
8. S. Aoyama (Honda) +0.502secs
9. Luthi (Aprilia) +0.642secs
10. Bautista (Aprilia) +0.658secs
20. Laverty (Honda) +3.823secs
26. Linfoot (Aprilia) +6.197secs