Speaking at the 'Ride with Brad' sportive in Lancashire on Sunday, Wiggins admitted that he would like Cavendish to stay "from a selfish point of view" but doesn't think it's a likely outcome due to Sky's general classification ambitions for the major races.
"On a personal level I have enjoyed riding with him this year and I enjoy his company, but I understand why he would probably have to leave," the 32-year-old explained.
"I love seeing him win as much as anyone else and to see Mark back out on the Tour winning six, seven or eight different stages and challenging for the green, he probably has to go [to another team]."
Cavendish won three stages, with two leadouts at this year's Tour de France but was only able to rely on the support of Bernhard Eisel, unlike his previous experience at HTC-HighRoad where he had the majority of teammates at his disposal.
"At Sky we have set a precedent now," Wiggins continued. "If we are going to dominate cycling and win three grand tours in a year, we have to start building to that GC thing.
"Unfortunately for Mark, as we saw in the Tour, the two don't really go well together."
Sky team principal Brailsford told the BBC following the end of the Tour de France that it would be reiterated to Cavendish that the team's focus would remain on Wiggins and Chris Froome and that discussions would take place to see how the Manxman "feels about that."
Cavendish has since been linked to Omega Pharma-QuickStep and Orica-GreenEdge.