Ben O'Connor has described the organisers of the Giro d'Italia as "dinosaurs" and the race as "one of the worst-organised" after riders forced a change in the route amid miserable weather conditions in the Italian Alps.

Even with 80km shaved off the stage, it was still slightly too long for the Australian, who suffered during a steep finishing climb to lose time in his pursuit of a place on the podium on Sunday.

Nothing, however, seems to trouble Tadej Pogačar, who won his fifth stage of the 16 so far contested, racing away from the other general classification contenders in the final kilometres of the summit finish at the Dolomites ski resort of Val Gardena.

That extended his lead to seven minutes, 18 seconds and he seems certain to finish in Rome wearing the maglia rosa.

Giulio Pellizzari, the last of a breakaway group to keep Pogačar at bay, was second on the day. The 20-year-old asked Pogačar for his sunglasses at the finish line and the Slovenian gave him his pink jersey too.

Dani Martinez finished third on stage 16, and was able to overtake Britain's Geraint Thomas into second place overall in the Giro.

O'Connor had moved to within 51 seconds of Martinez but is now 84 seconds behind the Colombian, though only 62 behind Thomas whom he finished alongside on Tuesday.

Freezing rain and snow in the Italian Alps meant the stage from Livigno, which had been scheduled to climb to almost 2,500 metres, was changed and delayed.

It had been altered last week due to the risk of avalanches, but the deteriorating conditions prompted riders to vote on skipping the Umbrail Pass and a treacherous 20km descent, citing safety issues.

Confusion and anger reigned in Livigno before organisers decided on incorporating the climb but not the descent, which would be done in cars. That was then scrapped and replaced by a roll out of Livigno followed by a long neutralised period.

But the riders, many of whom had been sheltering under canopies from the snow, refused again as they wanted to avoid getting even colder and wetter before a transfer to the proper start point.

"Despite a handshake between the parties, the athletes did not show up at the start in Livigno," organisers RCS said in a statement.

O'Connor was scathing as he put the riders' viewpoint to Eurosport.

"It's probably one of the worst-organised races I think and I'm just being honest. This would never happen in 99 per cent of other situations.

Giro d'Italia director Mauro Vegni told Italian TV, "The mountains are like this, sometimes you have to face certain situations. Obviously, if you ask the riders if they like riding in rain and snow, they'll say no."

O'Connor was not enamoured with Vengi's stance.

"I'd like to see him [Vegni] in our position, go outside on the bike and do the start of the stage and see what his answer is after those couple of hours," retorted O'Connor.

"I wish he could experience it as he would have a sense of what it is like rather than doing it in his car and saying 'this is great for people to watch.'"

AAP