Casey Stoner will start Sunday's Malaysian Grand Prix from the head of the second row after 'everything that could go wrong did go wrong' during the crucial second part of Saturday's qualifying session at Sepang.

The Ducati rider, second and first in the two races since his MotoGP comeback, was visibly disappointed at the end of the session - having gone from fighting Valentino Rossi for pole during the first part of the hour, to fourth and 0.9sec behind by the end of the session.

Stoner's best time came on just his seventh lap of 18, when he was riding with the hardest compound tyres which had, respectively, 25 laps on the front and 14 on the rear.

Afterwards, he explained what had happened.

"I'm really disappointed with that session because I know we could and should have been fighting for pole position," he began.

"I had a much better feeling with the setting at the start of the session but midway through we went to change tyres and after that we suffered from a huge vibration in the bike.

"We still haven't worked out what it is yet so we need to figure it out and fix it for tomorrow.

"I tried the softer compound but the chattering was even worse. I swapped to my other bike but we had a different setting in it that I hadn't tried and I didn't feel comfortable.

"Everything that could go wrong in the crucial second part of the session did go wrong, but if we can fix this problem then we'll be in good shape for tomorrow.

"Anyway I'm happy with my pace in race conditions and I look forward to tomorrow," he concluded.

Team-mate Nicky Hayden will start seventh on the grid, just 0.062sec shy of Toni Elias and a second row start.

"I didn't actually make as big a step this afternoon as I had hoped from the morning session," said the American. "On race tyres in the hotter temperature it was certainly tough and I was struggling a little bit.

"We had a couple of problems during the session but in the end I was able to find one good lap to get me into a respectable grid position, very close to the second row. I'm not too happy with my race pace - we're missing a few tenths and we have some work to do tonight to try and find where we can make them up.

"I'm never really happy with seventh place but to be honest today it was a pleasant surprise because it could have been much worse off than that if we were just a few tenths slower.

"We've got a big job to do tomorrow. 22 laps around here when your race pace isn't perfect is certainly not easy but that's what we train for. Hopefully we can improve in the warm-up, get a good start and we'll see what we got for them."