The Giro d'Italia race director says he was "very upset" by cyclists' safety protests and promised "consequences".
Riders completed more than half of stage 19 on their team buses after concerns were raised over racing in heavy rain, risking riders' health.
Organisers agreed with the Professional Cyclists' Association (CPA) to start 124km from the finish in Asti.
Czech rider Josef Cerny of CCC won the stage, while Britain's Tao Geoghegan Hart remains third overall.
BBC Sport understands organisers RCS were mystified by the action because it said riders had not voiced concerns to the race management earlier. Instead, it said, a few riders approached them 10 minutes before the start of the 258km race from Morbegno.
The CPA, which represents the cyclists, said on Friday before the stage began: "The riders' health is the priority, especially in this Covid period."
It added: "Reducing the stage will not diminish the show, but will allow the immune defences of the riders not to be put at greater risk."
However, race director Mauro Vegni told Eurosport: "[I'm] very upset about the way it's happened. It isn't the right way to resolve these issues.
"I think there are going to be words with lawyers - I don't think it's respectful to the race or people who want to watch.
"Today the parcours [course] was lovely. There will be consequences because of the behaviour of the riders."
Competing in heavy rain can cause riders, whose immune systems may already be compromised by excessive exertion, to become unwell as dirt and bacteria from the road is sprayed through the peloton.
Many riders were concerned it would increase the risk of contracting coronavirus.
Vegni added: "The stage was announced a year ago. A rainy October day is not an unusual thing and it is 13C, so not cold. There's no excuse not to do it."
The stage initially took place under heavy rain in the neutral zone before the official start, where riders were stopped and the team's buses were called to pick them up.
The peloton was eventually dropped off in Abbiategrasso, where, in drying conditions, a breakaway of 14 riders, including Britain's Alex Dowsett of Israel Start Up Nation, stayed ahead of the peloton for the duration.
Cerny broke clear of the break and held them off to cross the finish line 18 seconds ahead of Belgium's Victor Campenaerts of NTT and Italian Jacopo Mosca of Trek-Segafredo.
The peloton rolled in 11 minutes later after Bora-Hansgrohe called off their attack for Slovak Peter Sagan part-way through the stage.
Sunweb's Dutch rider Wilco Kelderman continues to lead the overall standings by 12 seconds from Australian team-mate Jai Hindley, and 15 seconds from Geoghegan Hart of Ineos Grenadiers.
Meanwhile, Vini Zabu-KTM's Italian rider Matteo Spreafico has left the Giro, having being suspended by the UCI - cycling's world governing body - after two adverse analytical findings for the prohibited substance enobosarm.
"The rider has the right to request and attend the analyses of the B samples," said a UCI statement.
"In accordance with the UCI anti-doping rules, the rider has been provisionally suspended until the adjudication of the affair."
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