Thomas still leads his Team Sky mate and defending champion Chris Froome by 1 minute, 39 seconds and Dutchman Tom Dumoulin by 1:50 going into Wednesday's 17th stage, a brutal 65-km, up-and-down trek from Bagneres-de-Luchon to Saint-Lary-Soulan.
"The police had to use tear gas on the protesting farmers...some of which has gone into the eyes of the riders, so the race has stopped for now", Team Dimension Data, one of the teams racing, tweeted when the race came to an abrupt stop.
The 218-kilometer stage from Carcassone to Bagnères-de-Luchon in the southwest of France was the first to hit the Pyrenees mountains, and was packed full of incidents. Tour organizers said police used tear gas to move the protesters as the peloton approached. Froome was treated with eye drops and Sagan poured water over his face to clean his eyes.
Prudhomme says it was irresponsible to further endanger the riders as he pointed to dramatic crashes suffered during the stage by Philippe Gilbert and Adam Yates, who both went down on descents while leading the race in separate incidents.
Froome and Thomas wash their eyes out. I took a lot of risks. "Everyone's doing the best they can and hopefully everyone can just behave and let us race".
The gas was used to disperse the protesters, but it ended up blowing in the direction of the peloton, which led to the race being stopped at the 187km-to-go point.
"Their field is the road, the road is open - we can not lock them in a swimming pool or a stadium or in a tennis court". "People should not block the road, no matter what causes they are fighting for".
"I felt a tingle in the eyes, and in the back of my throat". "I heard some of the guys had problems so I thought it was a good decision to stop and wait and bring everything together".
According to French media, the small group of farmers from the local Ariege department protested against the reduction of European Union funding.
The Tour's official Twitter account warned protesters they could face up to three years in prison for interrupting.
Froome was jostled and spat at on Alpe d'Huez, while 2014 victor Vincenzo Nibali saw his race ended after he was brought down in a tangle with a fan on the same mountain.
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