Kiwi cyclist Dion Smith has fallen just short of regaining the polka dot jersey on stage six of the Tour de France.

Smith became the first New Zealander to wear a distinctive jersey at the Tour after stage two, but lost the jersey worn by the King of the Mountains leader to Latvia's Toms Skujins on stage five.

However, this morning Smith managed to get in the breakaway, and was the first rider over the first two categorised climbs of the day, temporarily moving back into a share of the lead.

To take back the jersey, Smith needed to be one of the first two riders to reach the top of the first Mur-de-Bretagne climb, but with just under a kilometre left of the testing 6.9 per cent gradient, he was mopped up by the peloton, with Skujins popping out of the bunch to claim the points and remain two points ahead of Smith in the classification.

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"Tough day in the break today for me," said Smith. "I went chasing the KOM points again but came up short."

Smith, who claimed a superb ninth place on stage four, believes there are more chances ahead for him, with two flat stages upcoming before the race heads first to the cobbles of Roubaix, and then into the mountains.

'It's all good, [I'll] live to fight another day. It's a long tour ahead so more opportunities, we'll see how it goes."

New Zealand riders were in the thick of things throughout stage six, with Jack Bauer attacking after Smith was caught. Bauer snuck away from the peloton with 15 kilometres to go, and briefly held a 30 second lead, but he was eventually reeled in with just under four kilometres remaining as the second and final ascent of the Mur-de-Bretagne loomed.

At that point, the general classification contenders took over, with Ireland's Dan Martin attacking with a kilometre to go, and riding away for his second Tour de France stage win.

"I saw the moment. I had really good legs and when I went my legs kept coming and coming," Martin said. "I knew if I could get a gap it would be difficult to close from behind."

So it proved, with Pierre Latour finishing second after a desperate chase, and the majority of the GC contenders crossing three seconds behind Martin.

Four-time champion Chris Froome finished eight seconds after Martin in 18th, but the biggest losses were suffered by Romain Bardet and Tom Dumoulin. Dumoulin suffered a horrendously timed puncture with five kilometres to go, losing 53 seconds, while he was also penalised 20 seconds for drafting behind his team's car. Bardet had a mechanical issue, and while he re-joined the peloton, he paid for his effort and lost 31 seconds on the final climb.

"I had to chase and that effort was fatal. It's never good to lose time," said Bardet, who has finished second and third overall in the last two Tours. "There are a lot of twists on the Tour and this time luck was not on our side."

Greg Van Avermaet finished alongside the favourites to retain the yellow jersey by three seconds, and is now favoured to keep it as the Tour returns to flat sprint stages for the next two days.