Ash rained down on Catania and surrounding villages in the early hours of Thursday (local time) after the volcano became active, opening a crater pit on one side.
The ninth stage features two climbs on the volcano, including at the finish line at 1,892m above sea level.
"Sunday's stage is not at risk," Race director Angelo Zomegnan said in a statement.
"The stretch in question is only that of the last 6.5km on Etna. But onsite teams are already working to clear the road."
In the sixth stage, Francisco Ventoso of Spain edged Italian specialist Alessandro Petacchi in a sprint finish.
Ventoso led home a mass sprint to win the 216km stage from Orvieto to Fiuggi in 5 hours, 15 minutes, 39 seconds.
"This is the stage that I identified before the race," Ventoso said. "It was very long and very hard, but I kept going to the end and got it.
"Danilo (Di Luca) went out with 150 to 100 meters to go and I just tried to stay with him. Petacchi then tried to pass me, but he couldn't keep up."
Petacchi appeared to be headed for his second stage win of this year's Giro when he went head to head with Ventoso to the line. However, he abruptly stopped pedaling just before the finish and freewheeled across the line.
Roberto Ferrari of Androni was third with the same time, while three-time Tour de France winner and race favorite Alberto Contador finished 39th in the same time.
Pieter Weening of the Netherlands retained the pink jersey, two seconds clear of Kanstantsin Sivtsov of Belarus and Marco Pinotto of Italy after more than 20 hours, 15 minutes.
"We had a good day," Weening said of his Rabobank team. "Everyone was strong and tomorrow we will try to do the same and hopefully I will get another day in pink.
Contador was ninth, only 30 seconds behind.
"Tomorrow's stage is short," Contador said. "We will see who is doing well, but those who are in bad condition will be exposed. That said, I think the closing climb is not too demanding."
Jussi Veikkanen, Kristof Vandewalle, Yaroslav Popovych, Sacha Modolo and Frederik Veuchelen made the first break of the day, and even after dropping Modolo they still led by 90 seconds at the 15km mark.
Vandewalle went alone with 9km to go but was passed by the group less than 2km from the finish.
The Giro finishes in Milan on May 29.