Valentino Rossi, first and third in the pair of free practice sessions in Malaysia, dropped back to sixth in Sepang qualifying after struggling with the softer option tyre.
The Italian, fastest on Friday, was consistently in the top three during the early stages, but slipped back to sixth towards the end.
"With the hard tyre we're not so bad, even if we're lacking some grip and the bike is moving a bit, so it's not so easy to control. However with the softer tyre we suffered a lot more because the movement became bigger and I couldn't use the extra grip. This means I am only on the second row," he explained.
"Tomorrow's race will be very hard, maybe the hardest of the season because the temperature is unbelievable and starting from the second row will make it even harder, but we will do our best and hope to make a good start."
"We expected a better result than this today and our potential was greater, so we're a bit disappointed," confirmed Fiat Yamaha team manager Davide Brivio.
"Unfortunately at the end of the session the soft tyre didn't give us as big an advantage as we were hoping for so we couldn't do better than the second row, but we will try to improve for the race."