The Kazakhstani outfit have been plagued by failed drugs tests, with Artur Fedosseyev the latest to return a positive sample.
He joined fellow Astana riders Ilya Davidenok, Viktor Okishev, Valentin Iglinskiy and his brother Maxim, all of whom have been involved in similar incidents in the last two months.
But Nibali, who won four stages of this year's Tour, insists he will not quit Astana.
"I don't think I'd leave," the Italian told Cycling Weekly.
"I have my technical staff here, the people I wanted in the team. There's a good group, all around me and united."
The Union Cycliste International launched an investigation into Astana following the violations from Davidenok and the Iglinsky brothers and has the power to revoke the team's WorldTour licence.
Nibali, though, is confident that will not happen.
"The WorldTour licence for me is going to be okay," he added. "In this moment, I don't think there will be a problem."