The 30-year-old left Leeds to begin his preparations for the African Cup of Nations in Ghana last week, and Leeds will be without his services until the beginning of February.
Wise said: "We've been very open with each other. Rui knows that he's got another contract here. But does he want to sign a new contract on League One money when there's a possibility that we'll go up, or does he want to sign a contract on Championship money?
"If he wants to sit down when he comes back then he can, but I told him he'd be a fool. He'd be mad to do it now because we only pay a certain amount of money. Obviously if we go up we'll pay that little bit more.
"I'm just being honest with him, and he's said that he'll wait until the end of the season."
Marques finally made his league debut for the Whites against Coventry City on New Year's Day 2007, and he has been ever present during Leeds' League One schedule this term.
The centre-back, who was signed by Leeds in the summer of 2005, made just one appearance for United before Wise took charge in October 2006, but he is now on his way to passing his 50th club appearance before the end of this season.
Wise said: "He'll get a new contract even if he gets injured because I'm very loyal to him. "I gave him a chance and I like him as a player. I don't think anyone expected him to do as well as this. He's got better and better. He knows he's getting a contract, and he enjoys it here. He's got no intentions of going anywhere."