The 31-year-old has been linked with a move away from the club in recent weeks.
Duffen told the Hull Daily Mail: “Any player who can see they are unlikely to get first-team football is going to start considering their future and what is best for them.
“Wayne is a consummate professional and he has been an absolutely fantastic servant for Hull City.
“He’s not the sort of player who is happy not to be playing first-team football, but at the minute he knows he’s not going to get that action.
“That’s no reflection on Wayne as a player, it is just a fact of life that we have brought in two excellent centre-halves.
“Wayne now looks at the competition for places and he knows Anthony Gardner and Kamil Zayatte are ahead of him in the selection process for the first team at present.”