Brailsford took aim at spectators who have jostled and spat at his riders during the race when he said on Monday that it does not happen at other races and was uniquely French.
That led to UCI president David Lappartient, a Frenchman with whom Brailsford has already had a number of run-ins, criticising the Sky boss for "fueling the fire", and on Wednesday Brailsford took his words back.
"I'm a Francophile," he said. "I think anybody who knows me knows that wasn't my intension but I was pretty agitated about the attention we were getting.
"Of course I don't believe that spitting is a French cultural thing, but my point was that we only get that kind of thing at the Tour de France."
If he was sorry for his choice of words, Brailsford reiterated his concerns over security on a day when Geraint Thomas extended his lead in the Tour despite a spectator apparently trying to grab him in the final few hundred metres of stage 17, on which he finished third.
Chris Froome was also knocked off his bike by a gendarme who had mistaken him for a fan attempting to ride the course as he headed back to the team bus following the stage.
"My intention was never to criticise, just to draw some attention to the fact that I was getting pretty worried about our guys," Brailsford added.
"The issue is security and I was trying to bring that to everybody's attention. I feel very strongly about the security of this team. I chose to bring young Egan (Bernal) here and then half way through I thought I might really regret that decision - and that was nothing to do with racing his bike, or performance, it was just about the experience he was having."
Brailsford also mentioned the volatile atmosphere at the race when discussing Gianni Moscon, who was disqualified from the Tour on Sunday after lashing out at another rider, Fortuneo-Samsic's Elie Gesbert.
Brailsford is due to decide if the 24-year-old, who already has a lengthy disciplinary record, should face further punishment after the Tour is over.
"He's very, very talented," he said of Moscon. "This was a volatile environment and I selected him to come here and I take responsibility for bringing him here. It's been a difficult challenge to deal with. I'm 55 years old, I should know better myself. If I'm finding it challenging then these young lads are going to find it even more so.
"I don't want 'Brailsford thinks crowd contributed to Moscon behaviour' because that would be a step too far. I'm putting the Moscon thing behind me for now and I'm focusing on the guys who deserve all this attention. I'll come back to him after and draw some conclusions after that."
