Kallio won the 125cc Japanese Grand Prix for KTM in 2005 and 2006 - while KTM also won last year's 250cc event with team-mate Hiroshi Aoyama.
That run continued at a wet 2007 event, in which both Kallio and Hiroshi Aoyama charged quickly towards the front - and were soon locked in a victory battle with Honda team-mates Andrea Dovizioso and Yuki Takahashi.
Takahashi, a race leader in the middle stages, lost the advantage to Kallio with seven laps to go - then ran off track - while Hiroshi Aoyama fell from a close third, behind Kallio and Dovizioso, with three laps remaining.
Mika extended his lead in the closing stages as Dovi settled for a safe second - reducing Jorge Lorenzo's championship lead from 51 to 36 points with three rounds to go.
The reigning world champion and 2007 title leader endured a disappointing day, quickly slipping backwards through the pack on his way to an eventual eleventh place.
Race results – Motegi:
1. Kallio (KTM)
2. Dovizioso (Honda) +4.893secs
3. Barbera (Aprilia) +21.527secs
4. Takahashi (Honda) +23.488secs
5. de Angelis (Aprilia) +25.378secs
6. Simon (Honda) +42.264secs
7. Simoncelli (Gilera) +48.782secs
8. H. Aoyama (KTM) +57.782secs
9. S. Aoyama (Honda) +1min 9.049secs
10. Luthi (Aprilia) +1min 10.837secs
19. Laverty (Honda) +1 lap
Linfoot (Aprilia) DNF