"The riders of the Tour, the champions of this race, need to be respected".
The incidents have made some teams worry that fans are getting out of hand on the most famous climbs of the Tour.
After most of the other top sprinters at the Tour de France succumbed in the Alps, Peter Sagan was in prime position to dominate Friday's (Saturday's NZT) flat finish.
"It did worse than wind Merckx: It ruptured the fragile pact, the bond of trust that exists between the riders and the public", Bicycling.com's Richard Moore wrote in 2015.
After overzealous fans marred Thomas' win on Thursday atop the Alpe d'Huez, the otherwise complete calm of Friday's leg was briefly disturbed by a man on the roadside who tossed a smoke bomb into the centre of the peloton as it passed by with 16 kilometres left.
More recently, Team Sky rider Richie Porte claimed he was punched by a fan during a mountain stage in 2015 and later had words with a fan who yelled "Doper!" at him as he was riding back to the team bus at the end of the stage.
He managed to get back on the bike and bridge the gap to the leaders, leaking just 13 seconds to the triumphant Geraint Thomas, but called it a day after learning the extent of his injuries.
Frenchman Romain Bardet, one of the main title contenders who lies fifth overall and 3:07 off the pace, said the Tour was a popular party and should remain so. Prudhomme singled out selfie-taking fans - suggesting that officials could ban them from running behind the riders during the mountain stages - and those who lit flares along the course. "They make the riders breathe in noxious air, and they blind them", he added.
Defending champion Chris Froome finished fourth, also three seconds off the pace, as boos came from the crowd.
World champion Sagan was fastest down the final stretch, crossing the line ahead of Alexander Kristoff and Arnaud Démare in a bunch finish in Valence.
Twenty-four hours after four-time victor 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.
Tom Dumoulin stayed third overall at 1:50 behind.