Riding on the Bugatti circuit at Le Mans, Kallio finished with a clear margin of 0.3s over Italian rival Marco Simoncelli who was second fastest.
Joining Kallio on the provisional front row of the grid was Hungarian teammate Gabor Talmacsi who was third fastest, just six hundredths of a second behind Simoncelli.
With another strong performance the Red Bull KTM squad finished with three riders on the first two rows of the grid with Spanish teenager Julian Simon seventh fastest.
The session was conducted in cool and heavily overcast conditions, with rain threatening, although the track remained dry.
In a final surge of fast times Kallio, Talmacsi and Simon all recorded their best times on the final lap.
For the first time this season the KTM squad has six identical machines in the garage for their three factory riders.
Previously there had only been three bikes at the top specification. Engine updates for this race include new reed valves.
MIKA KALLIO #36 - First- (1'43.693)
"My bike was very stable and very fast, thanks to the new parts we have for this race, the only problem I had was a little bit of chatter at the front. Now I just hope the weather stays dry for final qualifying so that I can try and hold pole position. Everything is OK, although Le Mans is not my favourite track, it is stop-go with many slow corners."
GABOR TALMACSI #14 -Third - (1'44.073)
"It's nice, I'm on the front row again and this is a real boost for my confidence, the KTM is fast at every track we go to, always in the top four, either wet or dry. The set-up is OK, perhaps I just need some small changes at the rear but I did some good laps on race tyres today. I'm happy because I've never had much luck on Friday the 13th, but today was good for me!"
JULIAN SIMON #60 - Seventh - (1'44.325)
"I like this track and I had no problems today although I felt as if my bike was a little down on top speed. The set-up and tyres are OK although I think I can be faster tomorrow in final qualifying, now I just hope the rain stays away and the track is dry."
HARALD BARTOL - Managing and Technical Director
"A very good day by both the riders and the team. We now have six machines in identical specification, which helps our set-up work, and for this race new reed valves for the motors."
Source: KTM-Sportmotorcycle AG
Photographer: O. Bergamaschi