Repsol Honda's Marc Marquez is feeling confident he has the pace to challenge the factory Yamaha riders for victory at the Japanese MotoGP.

Marquez will start from the middle of the front row after qualifying second fastest behind Valentino Rossi, with Jorge Lorenzo completing the top three in Q2 for the Movistar team at Motegi.

The world championship leader holds an outside mathematical chance of clinching his third premier class crown on Sunday, with Marquez currently 52 points clear of Rossi.

The Honda rider is happy with his race pace at a track where he has previously found it harder to run with the factory Yamaha riders.

"Already this morning I was very happy because yesterday - okay, we were fast - but I didn't feel the best feeling with the bike but this morning we had a big improvement. This afternoon in FP4 we tried a few but for the qualifying we came back and it felt strong," said Marquez, who made a mistake on the brakes on a hot lap during Q2 before slackening off during his final pole attack when he came across yellow flags following Cal Crutchlow's minor slip off.

"I did a mistake with the second tyre but I'm very happy because this circuit is one of the most difficult for us during all the season and we are there, we are very close and consistent on the lap times. It's nicer to be in the position of Valentino in pole position but we are on the front row and that is the main target.

"Race pace is when I felt slightly better and it looks like with a new tyre especially, I struggle a little bit to find the feeling on the brake point but then when the tyre drops a little bit I am able to make the limits better. We will see tomorrow how the weather is and with higher temperature it looks like the Yamaha is stronger or closer but anyway I feel okay."

Marquez has already confirmed his tyre choice for the race, when he intends to run the medium front and soft Michelin rear on the RC213V.

"I think everybody will be with the medium front and soft rear. I tried the hard front this afternoon and it has some potential, it is good, but I don't want to take the risk. I prefer to have some warnings and some feedback and I will go with the medium front and soft rear," said the two-time MotoGP champion, who expects Rossi and Lorenzo to be the main contenders for victory on Sunday.

"You have to wait until after warm-up but at the moment I expect a tight fight with both Yamaha riders because it looks like they are the strongest ones. Then you have more riders but I feel both Yamahas are the strongest like every year here, but this year I am happy because I can be with them," he said. "I will see. My target is to finish in the podium tomorrow."

Reflecting on his decision to slow on his final lap in Q2, Marquez said he preferred to forgo the chance to snatch pole rather than risk crashing during a yellow flag situation.

"After 2013 in Silverstone, any time I see a yellow flag I slow down. I know it was the last lap of the qualifying and I was keen to push but I saw many people there and also Cal. [It was] too much risk and I lost the lap but I prefer this than have a crash and be like Silverstone."

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