The 129.9-km stage from Albertville to La Plagne was due to include the ascent of the Col des Saisies, but the climb has now been scrapped to avoid the affected zone, ASO said in a statement.
"In light of the distress experienced by the affected farmers and in order to preserve the smooth running of the race, it has been decided, in agreement with the relevant authorities, to modify the route," ASO said.
The ceremonial start will take place as planned in Albertville, followed by a 7-km neutralised section before the official start an hour later than planned.
Riders will rejoin the original course shortly before Beaufort, at the 52.4-km mark of the initial route.
As a result, the stage will now be reduced to 95 km.
The shortened stage still finishes in La Plagne and comes just two days before the Tour concludes in Paris on Sunday.