The US Anti-Doping Agency (USADA) this week said Armstrong was at the centre of the biggest doping programme in sporting history, as it produced more than 1,000 pages of testimony to support its decision to ban him for life in August.
"We cannot be indifferent to what USADA has unmasked this week, it's a damning picture that's been drawn," Prudhomme said.
"What we want is that there is no winner," Prudhomme said of the seven years between 1999 and 2005 when Armstrong was victorious in the gruelling annual race.
Evoking what he described as a "lost decade", the Tour organiser quoted the 19th century French poet, novelist and dramatist Victor Hugo: "Those who live are those who fight."
"It's one the difficulties that the current anti-doping battle has built for itself. Cycling, with the UCI (International Cycling Union governing body) as the lead in this battle, have been pioneers," said Prudhomme.
"The biological passport, the number of tests and the increasingly efficient targetting means cheats are caught faster. We must continue down this route. There's no other way possible."
The USADA report could not have come at a worse time for Tour organisers as they prepare to unveil the route for the 100th edition next year.