The Spanish Althea Racing rider set a one minute 48.283 seconds lap around the 4.907km racetrack after going off track for a spell.
Second quickest was Jonathan Rea (Honda World Superbike Team) with Marco Melandri (BMW Motorrad Motorsport) third and Sylvain Guintoli (Team Effenbert Liberty Racing) fourth.
Czech rider Jakub Smrz (Liberty Racing Team Effenbert Ducati), who is on provisional pole, crashed after losing the front on a left hander to finish seventh.
The red and white diagonal crossed flags were shown twice in the session after light rainfall, as safety was key in the blustery conditions.
1. Carlos Checa - Althea Racing Ducati 1098R - 1:48.283
2. Jonathan Rea - Honda World Superbike Team Honda CBR1000RR – 1:48.677
3. Marco Melandri - BMW Motorrad Motorsport BMW S1000 RR - 1:48.705
4. Sylvain Guintoli - Team Effenbert Liberty Racing Ducati 1098R - 1:48.728
5. Davide Giugliano - Althea Racing Ducati 1098R - 1:48.953
6. Leon Camier - FIXI Crescent Suzuki Suzuki GSX-R1000 – 1:49.029
7. Jakub Smrz - Liberty Racing Team Effenbert Ducati 1098R - 1:49.152
8. Tom Sykes - Kawasaki Racing Team Kawasaki ZX-10R - 1:49.158
9. Max Biaggi - Aprilia Racing Team Aprilia RSV4 Factory - 1:49.301
10. Eugene Laverty - Aprilia Racing Team Aprilia RSV4 Factory - 1:49.307