The Japanese rider and defending champion was well under the lap record with a time of 48.334secs. His young team-mate Jonathan Rea didn't join him in slipping under the lap record in this session having already beaten it earlier in the day.
Leon Haslam is still on a roll following his first win of this season last time out at Mondello Park and was running in third place at the undulating Scottish venue. His name sake Leon Camier was on his tail in fourth place on the Bike Animal Honda.
The Stobart Honda team were running in fifth and seventh respectively with Tom Sykes ahead of Shane Byrne and Gregorio Lavilla splitting the pair of them in sixth place.
The Rizla Suzuki pair were running in formation with Chris Walker in eighth just ahead of team-mate Cal Crutchlow in ninth place. Both riders benefited from a track day hosted by their team last week allowing them to relearn the circuit on road going machines.
Dean Thomas on the Samsung Suzuki was tenth despite a tumble at the exit of the chicane. Aaron Zanotti was also out of luck as he tipped off at Hislop towards the end of the session.
BSB free practice results (2) – Knockhill:
1. Ryuichi Kiyonari
2. Jonathan Rea
3. Leon Haslam
4. Leon Camier
5. Tom Sykes
6. Gregorio Lavilla
7. Shane Bryne
8. Chris Walker
9. Cal Crutchlow
10. Dean Thomas