Race leader Geraint Thomas, his Sky team-mate Chris Froome and world champion Peter Sagan were among those affected as the race was stopped for 15 minutes.
Farmers had blocked the road with hay bales 29 km into the 218km stage from Carcassonne to Bagneres-de-Luchon, and police used a pepper spray when tackling the protesters in an effort to clear a path.
That spray was still in the air when the peloton arrived on the scene, with several riders requiring medical treatment to clear their eyes and throats.
Prudhomme said it was irresponsible to endanger further the riders as he pointed to dramatic crashes suffered during the stage by Philippe Gilbert and Adam Yates, who both went down in separate incidents on descents while leading the race.
“Do not add to danger for the cyclists,” Prudhomme said. “Their field is the road, the road is open – we cannot lock them in a swimming pool or a stadium or in a tennis court. They must be respected, they take enough risks for their job.
“Many representatives of the agricultural world have clearly criticised and condemned this intolerable action. Leave the road to the riders, respect them. When the road goes up, when it goes down, the French riders, the foreign riders, the yellow jersey, all of them.”
Froome said he was grateful that the race had been neutralised to allow riders to recover.
“I just sprayed some water in the eyes and water in the face,” the four-time Tour winner said.
“My throat, nose and eyes were burning afterwards, but I think quite a lot of riders were in a similar situation so I think we were all grateful for the temporary neutralisation just to have a couple of kilometres to clear our eyes, nose and throat out and then the race continued again.
“Thankfully the effects didn’t last long, but temporarily everything was stinging and burning but it wore off pretty quickly.”
Thomas added: “It was certainly unfortunate that it was still lingering around when we came through. I could feel it in my eyes, a little bit of tingling, I gave them a wash and rinsed my mouth out. I was kind of lucky it didn’t affect me too much.”
Though farmers’ protests and other such incidents are nothing new at the Tour, this year there is a heightened tension regarding race security.
Froome was jostled and spat at on Alpe d’Huez, while 2014 winner Vincenzo Nibali saw his race ended after he was brought down in a tangle with a fan.
The latest incident came at the start of a stage that was won by Julian Alaphilippe, who had been chasing Yates when the Lancastrian crashed just 6.5km from the finish.
Yates led on the descent into Bagneres-de-Luchon after attacking three kilometres before the summit of the Col du Portillon, cresting the mountain with a 22-second advantage.
The main contenders crossed the line in a group some nine minutes after Alaphilippe to mean there is no change at the top of the general classification.
Team Sky’s Thomas continues to lead by one minute and 39 seconds from Froome, with Team Sunweb’s Tom Dumoulin a further 11 seconds behind.