"I'm not leaving, even though I would have every right to," Nibali told La Gazzetta dello Sport on Friday.
Astana's future in the professional cycling ranks is hanging in the balance after the International Cycling Union (UCI) asked its Licence Commission last month to "undertake a full review of the management and anti-doping policies of the Astana Pro Team".
Two riders from Astana's top tier team, brothers Maxim and Valentin Iglinskiy, have recently tested positive for banned substances.
Three riders from the Kazakhstan outfit's Continental (second division) team have also tested positive this year, Artur Fedosseyev adding his name last week to a doping blacklist already featuring Victor Okishev and Ilya Davidenok.
All five cases have cast a shadow over the team run by former Tour de France podium finisher Alexandre Vinokourov, whose career was blighted by doping suspicion and a ban for blood doping in 2007.
Vinokourov on Thursday distanced himself from the Astana Continental team, which is run by the Kazakhstan Cycling Federation, and said it is "now suspended from competition".
In a statement to AFP on Thursday, Astana affirmed: "The Kazakh Cycling Federation is the administrative management entity that operates and runs the Astana Continental Team and they will issue an official statement in the near future concerning the team."
Despite the potential for his achievements to be overshadowed by recent events, Nibali - the first Italian to win the fabled Tour de France yellow jersey since deceased compatriot Marco Pantani in 1998 - said he was not about to quit.
"I'm sure I've made the right choice. I'm sure the team is going to be given its racing licence, but if some absurd reason that doesn't happen, I'm not leaving, even though I would have every right to," added Nibali.
"It's not just me who is tied up with this team. I have my inner circle of people. There's a group of about six or seven of us. Where do I go?
"Astana has invested in us and we feel good here. I believe in them and they believe in me."
Nibali, the 2013 Giro d'Italia champion who also won the 2010 Tour of Spain, called the recent cheats from Astana's Continental outfit "idiots".
"Let's be clear. Astana and Astana 2 (Continental) are two different things. We've had two (positive) cases with the Iglinskiy brothers, but that was a family affair," he said.
"The other three (riders) - I don't even know what they look like - are idiots. I don't know what they have been up to... maybe they were motivated by the idea of getting a contract here (with Astana) and earning a good wage.
"But that's their business. The team has already taken action. The Continental set-up has been suspended and (Dmitri) Sedoun has been removed."
Sedoun is a 'directeur sportif' or coach with both Astana and the Continental team.