Cal Crutchlow excelled again as Casey Stoner was quickest in practice for Sunday's Portuguese Grand Prix.
After the morning session was blighted by rain, reigning champion Stoner pipped Ben Spies in the dry afternoon.
British rider Crutchlow - - was third fastest, ahead of Dani Pedrosa and Jorge Lorenzo.
Valentino Rossi's struggles continued down in ninth place, two places behind Ducati team-mate Nicky Hayden.
Stoner said: "We did a few laps this morning to try to understand the bike, to make sure everything was working and like Jerez we wanted to see where the wet patches were on the track.
"Then this afternoon, unfortunately there were still areas of the track that hadn't dried out but we managed to get some good dry time, the bike seems to be working OK at this point and we have a fairly good idea of what we need to do tomorrow."
It was a good afternoon for Spies, who has struggled to two 11th-placed finishes so far this season, though team-mate Lorenzo will be disappointed to be down in fifth on his 25th birthday.
Crutchlow - who qualified fourth for the last race at Jerez - is aiming to be the first British rider to finish on a MotoGP podium in 12 years.
Last Sunday he was the first Brit to set the fastest lap in a race since Barry Sheene in South Africa in 1984.
The Coventry-born rider said: "I'm really happy with the pace I was able to set, especially because we know that some other guys put in a new tyre at the end to go a bit quicker.
"We were just concentrating on working on the race set-up and we still have plenty of margin to improve. The first two races have given me a lot of confidence and I am looking forward to carrying on the good start this weekend."
Earlier, Miguel Oliveira set the pace in the Moto3 class, while British rider Scott Redding came out on top in Moto2.
Portugal MotoGP second practice times:
1. Casey Stoner (Aus) Repsol Honda 1:38.396
2. Ben Spies (US) Yamaha 1:38.717
3. Cal Crutchlow (GB) Tech3 Yamaha 1:38.742
4. Dani Pedrosa (Spa) Repsol Honda 1:38.797
5. Jorge Lorenzo (Spa) Yamaha 1:38.930
6. Alvaro Bautista (Spa) Gresini Honda 1:38.959
7. Nicky Hayden (US) Ducati 1:39.029
8. Hector Barbera (Spa) Pramac Ducati 1:39.193
9. Valentino Rossi (Ita) Ducati 1:39.357
10. Andrea Dovizioso (Ita) Tech3 Yamaha 1:39.615