Appeals for calm among Tour de France spectators appeared to fall on deaf ears as a lit flare was tossed into the peloton before world champion Peter Sagan claimed his third stage victory of the race in Valence.

Twenty-four hours after four-time winner Chris Froome was slapped and apparently spat at by elements within the massed crowds on Alpe d’Huez, there was fresh trouble when a spectator threw the flare around 16 and a half kilometres before the finish of the 169.5km stage from Bourg d’Oisans.

Spewing yellow smoke, the flare appeared to be thrown over Team Sky’s riders, massed on the right-hand side of the peloton around Geraint Thomas in the yellow jersey, before bouncing across the road without bringing down anyone.

“I didn’t actually notice it,” Thomas said. “Sixteen kilometres to go, did you say? I was fully in the zone then fighting for position. It was pretty stressful so I had no idea.”

The incident came only hours after Tour director Christian Prudhomme called for calm at the roadside after events spilled over on the Alpe d’Huez on Thursday.

Froome was slapped by at least one fan and appeared to be spat at by another, before Vincenzo Nibali crashed after touching a spectator, fracturing a vertebrae to put him out of the race.

2016 Tour de Yorkshire Press Conference – Yorkshire Air Musuem
Tour de France director Christian Prudhomme appealed to fans for calm (Tim Goode/PA)

“We need to restore calm and respect all the riders,” Prudhomme said.

“It was a very annoying climb of the Alpe d’Huez. The riders on the Tour, and champions of the Tour, must obviously be respected, as they are by the large majority of the public.

“By the roadside it was very calm for 10 days, with only a few anti-Froome or anti-Sky placards. But at a stroke, it all went up again.

“I can only renew my appeals for calm, for common sense, with regards to the riders who make up the Tour de France.”

Speaking before the start of Friday’s stage, Froome called for riders to get more protection.

“I think the organisers had tried to put in a few special precautions to stop those kind of things happening,” he said.

“When you’ve got fans touching and interfering with the riders, who are doing everything to try and get up the climb, that’s not a situation anyone wants to see. That’s not acceptable.

France Cycling Tour de France
Egan Bernal leads Geraint Thomas and Chris Froome up the Alpe d’Huez on Thursday (Peter Dejong/AP/PA)

“I was pushed a few times but thankfully I stayed on my bike and didn’t get knocked off.

“(Appealing for calm) is a step in the right direction but I think there are more measures that can be taken, for sure.”

There had been fears about security on Alpe d’Huez with Froome still facing lingering ill-feeling among some cycling fans following the salbutamol case in which he was cleared of wrong-doing just days before the Tour began, while Sky have often faced a mixed reception in France due to their dominance of the Tour in recent years.

For a third straight day, Thomas heard some boos as he appeared on the podium to collect his yellow jersey in Valence.

Asked why, he said: “I think that’s a question for the people out there. I don’t know. We just train hard, work hard and come here to try to win the race. That’s a question for the people on the side of the road.”

The day’s stage came down to a sprint, though there were only a handful of real contenders after the Alps saw no fewer than five fast men eliminated from the race through missed time cuts or abandonments.

Bora-Hansgrohe’s Sagan picked up his third stage win of this Tour as he overhauled UAE Team Emirates’ Alexander Kristoff and Arnaud Demare of Groupama-FDJ in the final few metres to win by a wheel length.

“I think I left it a little bit late and I was a little bit behind in the final 600 metres,” Sagan said. “With the short climb I tried to bring myself to the front and stay on the wheel of Kristoff. I am very happy to beat them.”

The flare was the only thing that came close to upsetting a relatively quiet day for Thomas after the drama of his back-to-back mountain stage wins which thrust him into yellow.

“It wasn’t exactly a rest day but for sure it was a lot easier than the last three days,” he said. “It was nice to go on fast roads, the wind was kind to us and it was a good day to get ticked off. A welcome easier day for the whole peloton.”

With no change in the general classification, Thomas leads Froome by one minute and 39 seconds, with Team Sunweb’s Tom Dumoulin a further 11 seconds back.