"On a personal level I have enjoyed riding with him, but I understand why he would probably have to leave," Wiggins said.
"I love seeing him win as much as anyone else and to see Mark back out on the Tour (de France) winning six, seven or eight different stages and challenging for the green jersey, he probably has to go," he added.
Cavendish, 27, was part of the team that helped Wiggins become the first Briton to win the Tour but the Manxman enjoyed just three stage wins as team orders took priority.
He took his number of stage wins to 23 in this year's Tour, taking him to fourth on the all-time list, but his return was the lowest since his debut in the race back in 2007.
In 2011 Cavendish, who still has more than two years left on his Sky deal, had won the green jersey as top sprinter.
Wiggins also said on Sunday that next month he will race in the Tour of Britain, long regarded as a minor stage race compared to the Tour de France, Giro d'Italia and Vuelta a Espana. Team-mate Chris Froome is currently trying to win the latter.
Team Sky boss Dave Brailsford has stressed that Sky are targeting sustained general classification wins in those three grand tours which works against sprinter Cavendish whose strength is on the faster, flatter stages.
Wiggins added: "Sky have set a precedent now, if we're going to dominate cycling and try to win all three grand tours.
"I suppose we have to start building towards the GC and, unfortunately for Mark, as we saw in the Tour, the two don't really go well together."
Wiggins will be at the start of the eight-stage Tour of Britain in Ipswich on September 9 to say thanks to all his fans for supporting him during his stellar year.
"I'm doing the Tour of Britain now," the 32-year-old was quoted as saying by Sky Sports. "I'll try to stay fit between now and then so I don't embarrass myself. It'll be good."