Freezing rain and snow in the Dolomite mountains meant the stage from Livigno, which had been scheduled to climb to almost 2,500 metres, was changed at the last minute.
The deteriorating conditions in the mountains prompted riders to vote on skipping the Umbrail Pass and a treacherous descent, citing safety issues.
Confusion and anger reined in Livigno before organisers decided on a new start point with the stage distance at 121km from Lasa/Laas.
A statement from organisers RCS accused riders of failing to stick to an agreement to start the race in Livigno.
"The Extreme Weather Protocol Commission met yesterday to decide on the conditions for today's stage," RCS said.
"On today's meeting, an agreement was reached on moving the race from Livigno with a town parade. Despite a handshake between the parties, the athletes did not show up at the start in Livigno."
Riders had a different view with Ben O'Connor (Decathlon AG2R La Mondiale), calling organisers "dinosaurs."
"It's probably one of the worst organised races I think and I'm just being honest. This would never happen in 99% of other situations," O'Connor told Eurosport.
"It's just a shame that it is 2024 and you have dinosaurs who really don't see the human side of things."
The shortened stage, which still features tough climbs, began in heavy rain.
Tadej Pogacar has a commanding lead in the overall standings, six minutes 41 seconds ahead of Geraint Thomas.
Giro d'Italia director Mauro Vegni said organisers had listened to the riders' concerns.
"The mountains are like this, sometimes you have to face certain situations," he told Rai.
"We tried to provide additional safety measures for the riders but we agreed that if the conditions worsened we would have avoided the Umbrail Pass. And that's what happened.
"Obviously, if you ask the riders if they like riding in rain and snow, they'll say no. Everybody has his point of view and that's normal."
