Heavy traffic in Marseille city centre meant Astana broke the organizers' rule that teams must register for the stage at least 20 minutes before the start of the race.
The Kazakhstan-backed cycling team have been fined 65 euros for the infringement.
"How typical that this team were late. It is disrespectful to the public who came here just to see Armstrong," said race director Jean-Francois Pescheux.
"The money makes no difference to them.
"We will ask the UCI to make the fines harder."
Before the start, Armstrong was seen sharing a cup of coffee with actor Ben Stiller, who was visiting the Tour's VIP area on Monday morning.
Armstrong had a cameo role in the 2004 movie Dodgeball in which Stiller starred. It wasn't clear whether the coffee stop contributed to the delay in signing in.
Source: Velo News/ photo from supertouchart.com