Australian time trial world champion Rohan Dennis went AWOL for over an hour after abandoning the Tour de France and his Bahrain Merida team management had no explanation about his withdrawal during the 12th stage.

Key points: Australian rider Rohan Dennis quit the race midway through 12th stage without explanation

Australian rider Rohan Dennis quit the race midway through 12th stage without explanation Dennis had been instructed by his team to ride conservatively to save energy for the time trial

Dennis had been instructed by his team to ride conservatively to save energy for the time trial Bahrain-Merida says it is too soon to tell if there would be "consequences" for Dennis

Dennis, one of the favourites for Friday's individual effort against the clock, pulled out 80 kilometres from the finish of the 12th stage, organisers said.

The Australian's team, Bahrain Merida, was unable to locate him for over an hour and he was eventually spotted with his bike parked against the team bus near the finish line.

Bahrain-Merida even sent an alarming message out on social networks, saying all it cared about was "the welfare" of Dennis after Tour organisers announced he had pulled out of the race.

Dennis's withdrawal was even more surprising as it came a day before Friday's short time trial in Pau, where he would have been an obvious favourite alongside defending Tour champion Geraint Thomas, given Dennis's pedigree in the race against the clock.

The Australian ultimately resurfaced at the finish line in Bagneres-de-Bigorre, where British rider Simon Yates, the reigning Spanish Vuelta champion, posted his first stage win after a long breakaway that did not shuffle the overall standings.

According to French TV, Dennis was seen arguing with his team car before climbing off his bike, but sports director Gorazd Stangelj told reporters he "knew nothing about it".

"We are also confused. I'm disappointed about what happened. We actually expected a big effort from him tomorrow," Stangelj said.

"It was his decision today to stop in the feed zone. We tried to speak with him. He said, 'I don't want to talk' and just abandoned the race.

"His condition is not bad, he's good enough to perform at the Tour de France. For sure it has nothing to do with his condition."

Dennis's bike was pictured parked out the front of Bahrain-Merida's tour bus after he left the stage. ( Supplied: Robert Arnold )

Bahrain-Merida's main goal at the Tour this year was to fulfill former Tour champion Vincenzo Nibali's ambition to fight for a podium finish.

Asked whether Dennis was hard to work with, Stangelj said: "I didn't have any problem with him this season.

"He is a special guy, let's say all the champions are, he is really 100 per cent when he wants something and it's difficult to make everyone 100 per cent happy at the same moment.

"Now is the time to clear things up, to make decisions for the future," Stangelj added, however stressing it was too soon to tell whether there would be "consequences" for Dennis.

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Eventually, Dennis released a statement that failed to explain his reasons for quitting the race.

"I am very disappointed to leave the race at this point. Obviously the individual time trial tomorrow had been a big goal for me and the team, but given my current feeling it was the right decision to withdraw earlier today," Dennis said.

"I wish my teammates the very best for the remainder of the race and would like to thank all the Tour de France fans who cheered for me, at home and on the roadside, since Brussels.

"I will hopefully be back competing in this great race again over the coming seasons."

Yates sprints away for first Tour stage win

Dennis's extraordinary withdrawal was the talk of the day, but did not eclipse Yates's maiden win at the Tour.

The British rider launched a counterattack behind a group of fugitives in a technical downhill and was joined at the front by Gregor Muhlberger and Pello Bilbao.

The trio worked well together until the final sprint shaped up 200m from the finish line in Bagneres-de-Bigorre.

Yates launched the sprint, was first into the last turn and held off Bilbao for the victory.

As the Tour hit high mountains with two first-category climbs, the main favourites closely watched each other and did not attack, saving strength for the super hard days still to come.

The main pack of contenders crossed the finish line 9 minutes, 35 seconds behind the winner, with no major change in the overall standings.

Frenchman Julian Alaphilippe kept the race leader's yellow jersey ahead of Friday's time trial in Pau, 1 minute, 12 seconds ahead of Thomas.

AP/Reuters