"It's professional sport, and you expect professional athletes to play and entertain without being impacted on by the crowd.
"I know that this is part of the joy of our sport, how close the crowd gets, but we know that if impacts the race as it did today with Nibali then that's too much."
Sky's riders were accompanied by booing and jeering all the way up the Alpe d'Huez climb, with Thomas booed as he crossed the finish line and again as he was awarded the yellow jersey at the podium presentation.
Team Sky have been given a rough ride in France ever since they began dominating the Tour in 2012, and even more so since revelations about the Therapeutic Use Exemptions used by Sir Bradley Wiggins to win that first race.
There is a good deal of scepticism on the part of the French public regarding Froome, who has had to contend in the past with punches and even urine being thrown at him. The 33 year-old arrived here having just been cleared of any wrongdoing over a nine-month Salbutamol investigation, but even with Wada and the UCI saying he had no case to answer, fans at the team presentation in the Vendée booed the team.
Alpe d'Huez was always likely to be the flashpoint for the worst behaviour and so it proved, with punches and spit greeting the riders, although in truth it was probably no worse than it has been in recent years. Perhaps less rowdy in fact, with a strong police presence at Dutch Corner, where the fans were kept behind ropes for the first time, and barriers erected at the bottom of the climb.
Thomas said he did not see the punches aimed at Froome, but he pleaded for fans to be sensible.
"I didn't see that [the punch on Froome] but if people don't like Sky and want to boo that's fine, boo all you like," he said. "But just let us race. Don't affect the race, don't touch the riders, don't spit at us. Have a bit of decency, like. Just voice your opinion all you want but let us do the racing."