Nibali finished second to Froome in the Vuelta a España in 2017, where Froome tested for double the legal limit of asthma drug salbutamol after stage 18.
Froome and Team Sky both deny any wrongdoing.
"It's right that Froome defends himself with the best experts and lawyers possible," Nibali told Cycling Weekly.
"I've seen in the past with athletes that it's better not to race because if you race and the ban arrives, then you lose everything, all the results and suspension. But it's a decision for the team and the rider.
"Froome faces the decision. I would advise him as a friend, even if we are not that friendly, to make the best decision for this sport. For the fans and the current movement in cycling. He knows. He knows the facts and the process."
Nibali was due to start his season in Argentina at the Vuelta a San Juan on Sunday but he was sick the morning of the race and cancelled his plans. He will now travel back to Italy on Wednesday and begin his season at the Tour of Oman in Feburary.
The Italian talked long about his season ahead, with the Tour de France on the programme, but even more about Froome's case.
Froome said he took more puffs of salbutamol from his inhaler under doctor's orders during the Vuelta, and the four-time Tour winner is currently providing evidence to the Legal Anti-Doping Services (LADS) in a bid to avoid suspension.
"As it is now, everyone wants clarity. Sometimes there are mistakes made. I can't put myself in his shoes,” Nibali added.
"Chris made his remarks already. He said he followed the doctor's order and took more doses, so... So it's the doctor's fault. Maybe Chris was negligent to do so as a precaution.
"I don't want to say something, so it is 'Nibali says this or that', but we all ask that the time frame is shorter."
Nibali speaks little English, but follows Froome closely and bumps shoulders with him regularly in Grand Tours. Once, so heated the rivalry in the 2015 Tour, Froome rode to Nibali's team bus and went on to confront Nibali.
Between training in Argentina and at his home base in Lugano, Nibali checks the news. He read L'Equipe's report that Froome may argue a kidney problem led to a 2000 reading, well over the 1000 limit.
Froome is due to start his season mid-February, perhaps at the Ruta del Sol in Spain despite the advice otherwise from UCI boss David Lappartient and others like Romain Bardet and Nibali.
Nibali, who is one of the few riders with titles from all three Grand Tours, having won the Giro twice, the Vuelta once and the Tour in 2014, will skip his home race for an attempt at a second Tour de France title in 2018
He'll lead his Bahrain-Merida team, the first WorldTour team to take root in the Middle East, into its second year and will lead them for the first time at Tour.
The last time Nibali won the Tour in 2014, Froome crashed and abandoned in the opening stages and could not defend his first title from 2013. Many said Nibali won partly due to Froome's absence.
"This is just those who understand very little about cycling and who haven't followed my development and how I won races leading up to that day in 2014," Nibali said.
"Think about all the races I lost over the years or where I finished second by seconds because I was sick or crashed."
Nibali will face Froome, Movistar's Mikel Landa and Nairo Quintana (Movistar), Romain Bardet (Ag2r La Mondiale), Rigoberto Urán (EF Education First-Drapac), and Tom Dumoulin (Sunweb) in July.
"This is the beautiful thing in cycling how everyone is fighting among themselves, and you get different winners and not the same results all the time..."
Nibali paused for a second and added, "Besides this other rider who's always able to win. Froome? Well, he wins all the time, so yeah."
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