Kimi Raikkonen will be forced to drop 10 places on the grid for the Japanese Grand Prix after having to replace his engine during first practice.
Raikkonen has suffered several retirements this season
Flames and smoke were seen from the rear of the Finn's McLaren, which has been beset by problems this season.
The McLaren team began the week only two points ahead of Renault in the constructors' championship.
McLaren's Spanish test driver Pedro de la Rosa and Toyota reserve Ricardo Zonta headed the two sessions.
Raikkonen tried to remain upbeat after suffering his fourth punishment in nine races.
"Obviously I'm a bit disappointed with the engine failure, however, we managed to get in some running in the second and there is still plenty of time left on Saturday."
De la Rosa posted the fastest time in the first one-hour session, lapping in one minute 30.532 seconds.
Zonta was quickest in a rain-hit second in 1:30.682, ahead of Ferrari's Michael Schumacher and De la Rosa.
Schumacher, who has won four of the last five races in Japan, was just 18th after the first session after deciding to run on new tyres but improved massively despite running wide on the slippery track.
Jenson Button, in a Honda-powered BAR, was the quickest race driver in the morning with the third best lap but finished ninth overall in the afternoon.
The Briton was happy with his car's performance on the day but is concerned that tyre wear could affect his chances of success in Sunday's race.
"The car feels good. On one lap it has been very positive, but a lot of the long runs we have suffered with graining on the tyres.
"That is the problem we have to solve or we will not be strong in the race. But I think we are getting there," he said.
Renault's Fernando Alonso, who became Formula One's youngest champion at the last race in Brazil, lapped sixth fastest in the morning and eighth in the afternoon.
"We expected rain in the afternoon so we ran a lot in the first session," Alonso said.
1st free practice, session two, Suzuka:
1. Ricardo Zonta (Brazil) Toyota 1:30.682
2. Michael Schumacher (Germany) Ferrari 1:31.716
3. Pedro de la Rosa (Spain) McLaren 1:31.821
4. Rubens Barrichello (Brazil) Ferrari 1:32.267
5. Kimi Raikkonen (Finland) McLaren 1:32.849
6. Ralf Schumacher (Germany) Toyota 1:32.917
7. Jarno Trulli (Italy) Toyota 1:33.122
8. Fernando Alonso (Spain) Renault 1:33.259
9. Jenson Button (Britain) BAR 1:33.453
10. Mark Webber (Australia) Williams 1:33.520
11. David Coulthard (Britain) Red Bull 1:33.563
12. Antonio Pizzonia (Brazil) Williams 1:33.679
13. Takuma Sato (Japan) BAR 1:34.330
14. Giancarlo Fisichella (Italy) Renault 1:34.400
15. Felipe Massa (Brazil) Sauber 1:34.421
16. Christian Klien (Austria) Red Bull 1:34.707
17. Sakon Yamamoto (Japan) Jordan 1:34.829
18. Jacques Villeneuve (Canada) Sauber 1:34.874
19. Vitantonio Liuzzi (Italy) Red Bull 1:34.977
20. Robert Doornbos (Netherlands) Minardi 1:35.150
21. Tiago Monteiro (Portugal) Jordan 1:35.388
22. Juan Pablo Montoya (Colombia) McLaren 1:37.371
23. Christijan Albers (Netherlands) Minardi 1:37.626
24. Narain Karthikeyan (India) Jordan 1:38.034